diff --git a/.editorconfig b/.editorconfig
index b6b31907..b78de6e6 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index be0acf3c..d7271fd4 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cuta
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 0a5bf86b..ce560a55 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -15,9 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -28,3 +25,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 8e8011e1..7d897f56 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -23,3 +23,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 30f05d3d..ff515085 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -8,6 +8,11 @@ on:
   release:
     types: [published]
 
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   ##############################
   ### SMALL INTEGRATION TEST ###
@@ -18,17 +23,12 @@ jobs:
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}"
     runs-on: ubuntu-latest
     env:
-      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_VER: ${{ matrix.NXF_VER }}
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
-          # Test latest nextflow version
-          - NXF_VER: ""
+        NXF_VER: ["21.10.3", ""]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -70,7 +70,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ["21.10.3", ""]
+        NXF_VER: ["21.10.3", ""]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -106,8 +106,6 @@ jobs:
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
     runs-on: ubuntu-latest
     env:
-      NXF_VER: ""
-      NXF_EDGE: 1
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none
     steps:
@@ -115,10 +113,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-          nextflow self-update
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-everything"
 
       # Work around for the unexpected end of file error that github actions seems to get when downloading compressed
       # files during pipeline execution
@@ -141,34 +138,23 @@ jobs:
   ###      UNIT TESTS        ###
   ##############################
   unit_tests:
-    name: ${{ matrix.nxf_version }} ${{ matrix.tags }}
+    name: ${{ matrix.NXF_VER }} ${{ matrix.tags }}
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/cutandrun') }}
     runs-on: ubuntu-20.04
     env:
+      NXF_VER: ${{ matrix.NXF_VER }}
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ["21.10.3", ""]
+        NXF_VER: ["21.10.3", ""]
         tags:
-          - test_params
+          - test_genome_options
           - test_samplesheet
-          - verify_output_save_ref
-          - verify_output_only_input
-          - verify_output_save_merged
-          - verify_output_skip_fastqc
-          - verify_output_save_trimmed
-          - verify_output_skip_trimming
-          - verify_output_align_intermed
-          - verify_output_align_only_align
-          - verify_output_align_save_spikein_align
-          - verify_output_align_save_unaligned
-          - verify_output_only_filtering
-          - verify_output_align_duplicates_mark
-          - verify_output_align_duplicates_remove
-          - verify_output_align_duplicates_remove_target
-          - verify_output_peak_calling_only_peak_calling
+          - test_samplesheet_2
+          - test_filtering_noqfilter
+          - test_filtering_withqfilter
           - test_bam_scale_none
           - test_bam_scale_spikein
           - test_bam_scale_cpm
@@ -182,14 +168,37 @@ jobs:
           - test_peak_callers_macs2_seacr
           - test_peak_callers_seacr_macs2_noigg
           - test_peak_callers_ctrl_tests
-          - test_conseneus_peaks_group
-          - test_conseneus_peaks_all
-          - test_conseneus_peaks_invalid
+          - test_consensus_peaks_group
+          - test_consensus_peaks_all
+          - test_consensus_peaks_invalid
+          - verify_output_only_input
+          - verify_output_save_merged
+          - verify_output_save_trimmed
+          - verify_output_skip_trimming
+          - verify_output_skip_fastqc
+          - verify_output_save_ref
+          - verify_output_align_only_align
+          - verify_output_align_intermed
+          - verify_output_align_save_spikein_align
+          - verify_output_align_save_unaligned
+          - verify_output_align_duplicates_mark
+          - verify_output_align_duplicates_remove
+          - verify_output_align_duplicates_remove_target
+          - verify_output_only_filtering
+          - verify_output_peak_calling_only_peak_calling
+          - verify_output_reporting_skip_preseq_false
+          - verify_output_reporting_skip_preseq_true
+          - verify_output_reporting_skip_dtqc_false
+          - verify_output_reporting_skip_dtqc_true
+          - verify_output_reporting_skip_heatmaps_false
+          - verify_output_reporting_skip_heatmaps_true
+          - verify_output_reporting_skip_igv_false
+          - verify_output_reporting_skip_igv_true
+          - verify_output_reporting_skip_multiqc_false
+          - verify_output_reporting_skip_multiqc_true
+          - verify_output_reporting_skip_peak_qc_false
+          - verify_output_reporting_skip_peak_qc_true
           - verify_output_reporting_skip_reporting
-          - verify_output_reporting_skip_igv
-          - verify_output_reporting_skip_heatmaps
-          - verify_output_reporting_skip_multiqc
-          - verify_output_skip_frip
     steps:
       - name: Checkout Code
         uses: actions/checkout@v2
@@ -219,9 +228,6 @@ jobs:
             ${{ runner.os }}-nextflow-
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.nxf_version }}
-          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -229,16 +235,23 @@ jobs:
       - name: Run pytest-workflow
         uses: Wandalen/wretry.action@v1.0.11
         with:
-          command: pytest --tag ${{ matrix.tags }} --kwdof
+          command: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.tags }} --symlink --kwdof --color=yes
           attempt_limit: 3
 
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
       - name: Upload logs on failure
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          name: logs-unit-tests
           path: |
-            /tmp/pytest_workflow_*/*/.nextflow.log
-            /tmp/pytest_workflow_*/*/log.out
-            /tmp/pytest_workflow_*/*/log.err
-            /tmp/pytest_workflow_*/*/work
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 77358dee..8a5ce69b 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -35,6 +35,36 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
@@ -42,15 +72,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies
diff --git a/.prettierignore b/.prettierignore
index d0e7ae58..eb74a574 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,4 +1,5 @@
 email_template.html
+adaptivecard.json
 .nextflow*
 work/
 data/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8964bbbb..7c08fbb0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -103,3 +103,56 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 > **NB:** Dependency has been **added** if just the new version information is present.
 > **NB:** Dependency has been **removed** if version information isn't present.
+
+## [3.0] - 2022-09-26
+
+### Major Changes
+
+- Major rework of the pipeline internal flow structure. Metadata from processes (such as read counts) was previously annotated to a channel dictionary that was passed through the pipeline where various reporting processes could use the data. This was interacting with quite a few bugs in the Nextflow pipeline resume feature, causing lots of processes to rerun unnecessarily on resume. Any metadata generated in the pipeline is now written to files and passed where necessary to consuming reporting processes. This has drastically improved the number of processes that incorrectly rerun on resume.
+
+- Re-organized the pipeline into clearer sections, breaking related processes into sub-workflows where possible. This is for better readability, but also to prepare the pipeline for the major upcoming nf-core feature of re-usable sub-workflows. as part of this rework, the pipeline now has distinct sections for fragment-based QC and peak-based QC.
+
+- All reporting has been moved into MultiQC where possible. All PDF-based charting has been removed. Other PDF reports such as heatmaps and upset plots are still generated.
+
+- We have listened to user comments that there is no guide on how to interpret the results from the pipeline. In response, we have revamped the documentation in the `output.md` document to describe the reporting in much more depth including good and bad examples of reporting output where possible.
+
+- [[#140](https://github.com/nf-core/cutandrun/issues/140)] - IGV browser output has been reworked. We first fixed the performance issues with long load times by including the genome index into the session folder. IGV output now includes peaks from all peak callers used in pipeline, not just the primary one. Users can now select whether the gene track exported with the IGV session contains gene symbols or gene names. Several visual changes have been made to improve the default appearance and order of tracks.
+
+- Added PreSeq library complexity reporting.
+
+- Added full suite of fragment-based deepTools QC using the `multiBAMSummary` module. We generate three reporting from this fragment dataset: PCA, correlation and fingerprint plots. This has replaced our previous python implementation of sample correlation calculation.
+
+- All coverage tracks generated from reads now extend reads to full fragment length by default. We feel this creates more realistic coverage tracks for CUT&RUN and improves the accuracy of other fragment-based reports.
+
+### Enhancements
+
+- Updated pipeline template to nf-core/tools `2.5.1`.
+- [[#149](https://github.com/nf-core/cutandrun/issues/149)] - Pipeline will now use a blacklist file if provided to create an include list for the genome.
+- The FRiP score is now calculated based on extended read fragments and not just mapped reads.
+- [[#138](https://github.com/nf-core/cutandrun/issues/138)] - Better sample sheet error reporting.
+- Gene bed files will now be automatically created from the GTF file if not supplied.
+- The default minimum q-score for read quality has been changed from 0 to 20.
+- [[#156](https://github.com/nf-core/cutandrun/issues/156)] SEACR has been better parameterized with dedicated config values for stringency and normalization. Credit to `CloXD` for this.
+- deepTools heatmap generation has been better parameterized with dedicated config values for the gene and peak region settings.
+- Consensus peak count reporting has been added to MultiQC.
+- Reviewed and updated CI tests for better code coverage.
+- Updated all nf-core modules to latest versions.
+
+### Fixes
+
+- Fixed some bugs in the passing of MACS2 peak data through the pipeline in v2.0. MACS2 peaks will now be correctly used and reporting on in the pipeline.
+- [[#135](https://github.com/nf-core/cutandrun/issues/135)] - Removed many of the yellow warnings that were appearing in the pipeline to do with resource config options for processes that were not run.
+- [[#137](https://github.com/nf-core/cutandrun/issues/137)] - Fixed the `workflow.OnComplete` error.
+
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `multiqc`  | 1.12        | 1.13        |
+| `picard`   | 2.27.2      | 2.27.4      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+> **NB:** Dependency has been **added** if just the new version information is present.
+> **NB:** Dependency has been **removed** if version information isn't present.
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 00000000..017666c0
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Garcia
+    given-names: Maxime Ulysse
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Garcia
+      given-names: Maxime Ulysse
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x
diff --git a/README.md b/README.md
index dead8265..31649adf 100644
--- a/README.md
+++ b/README.md
@@ -6,14 +6,12 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5653535-1073c8)](https://doi.org/10.5281/zenodo.5653535)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
-[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
-[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/cutandrun)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23cutandrun-4A154B?logo=slack)](https://nfcore.slack.com/channels/cutandrun)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23cutandrun-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/cutandrun)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -31,7 +29,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 The pipeline has been developed with continuous integration (CI) and test driven development (TDD) at its core. nf-core code and module linting as well as a battery of over 100 unit and integration tests run on pull request to the main repository and on release of the pipeline. On official release, automated CI tests run the pipeline on a full-sized dataset on AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/cutandrun/results).
 
-![pipeline_diagram](docs/images/cutandrun-flow-diagram-v1-0_2.png)
+![pipeline_diagram](docs/images/cutandrun-flow-diagram-v3.0.png)
 
 ## Pipeline summary
 
@@ -46,11 +44,12 @@ The pipeline has been developed with continuous integration (CI) and test driven
 9. Create bigWig coverage files ([`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
 10. Peak calling ([`SEACR`](https://github.com/FredHutch/SEACR), [`MACS2`](https://github.com/macs3-project/MACS))
 11. Consensus peak merging and reporting ([`bedtools`](https://github.com/arq5x/bedtools2/))
-12. Quality control and analysis:
-    1. Alignment, fragment length and peak analysis and replicate reproducibility ([`python`](https://www.python.org/))
-    2. Heatmap peak analysis ([`deepTools`](https://github.com/deeptools/deepTools/))
-13. Genome browser session ([`IGV`](https://software.broadinstitute.org/software/igv/))
-14. Present QC for raw read, alignment and duplicate reads ([`MultiQC`](http://multiqc.info/))
+12. Library complexity ([preseq]([Preseq | The Smith Lab](http://smithlabresearch.org/software/preseq)))
+13. Fragment-based quality control ([`deepTools`](https://github.com/deeptools/deepTools/))
+14. Peak-based quality control ([`bedtools`](https://github.com/arq5x/bedtools2/), custom python)
+15. Heatmap peak analysis ([`deepTools`](https://github.com/deeptools/deepTools/))
+16. Genome browser session ([`IGV`](https://software.broadinstitute.org/software/igv/))
+17. Present all QC in web-based report ([`MultiQC`](http://multiqc.info/))
 
 ## Quick Start
 
@@ -60,7 +59,7 @@ The pipeline has been developed with continuous integration (CI) and test driven
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run nf-core/cutandrun -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
@@ -80,7 +79,7 @@ The pipeline has been developed with continuous integration (CI) and test driven
 
    - Typical command for CUT&Run/CUT&Tag analysis:
 
-   ```console
+   ```bash
    nextflow run nf-core/cutandrun --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
new file mode 100644
index 00000000..a2539c55
--- /dev/null
+++ b/assets/adaptivecard.json
@@ -0,0 +1,67 @@
+{
+    "type": "message",
+    "attachments": [
+        {
+            "contentType": "application/vnd.microsoft.card.adaptive",
+            "contentUrl": null,
+            "content": {
+                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "msteams": {
+                    "width": "Full"
+                },
+                "type": "AdaptiveCard",
+                "version": "1.2",
+                "body": [
+                    {
+                        "type": "TextBlock",
+                        "size": "Large",
+                        "weight": "Bolder",
+                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+                        "text": "nf-core/cutandrun v${version} - ${runName}",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "spacing": "None",
+                        "text": "Completed at ${dateComplete} (duration: ${duration})",
+                        "isSubtle": true,
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "The command used to launch the workflow was as follows:",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "${commandLine}",
+                        "isSubtle": true,
+                        "wrap": true
+                    }
+                ],
+                "actions": [
+                    {
+                        "type": "Action.ShowCard",
+                        "title": "Pipeline Configuration",
+                        "card": {
+                            "type": "AdaptiveCard",
+                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                            "body": [
+                                {
+                                    "type": "FactSet",
+                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}
diff --git a/assets/blacklists/GRCh37-blacklist.bed b/assets/blacklists/GRCh37-blacklist.bed
new file mode 100644
index 00000000..dcf5caff
--- /dev/null
+++ b/assets/blacklists/GRCh37-blacklist.bed
@@ -0,0 +1,411 @@
+1	564449	570371	High_Mappability_island	1000	.     
+1	724136	727043	Satellite_repeat	1000	.     
+1	825006	825115	BSR/Beta	1000	.     
+1	2583334	2634374	Low_mappability_island	1000	.     
+1	4363064	4363242	(CATTC)n	1000	.     
+1	5725866	5736651	Low_mappability_island	1000	.     
+1	16839923	16841396	Low_mappability_island	1000	.     
+1	38077347	38077423	Low_mappability_island	1000	.     
+1	91852785	91853147	LSU-rRNA_Hsa	1000	.     
+1	104163724	104163860	Low_mappability_island	1000	.     
+1	108112972	108113707	LSU-rRNA_Hsa	1000	.     
+1	121351474	121487059	centromeric_repeat	1000	.     
+1	142535434	142543081	Satellite_repeat	1000	.     
+1	142723256	142723968	Low_mappability_island	1000	.     
+1	142792613	142793303	Low_mappability_island	1000	.     
+1	142835822	142837333	Low_mappability_island	1000	.     
+1	143274490	143284340	centromeric_repeat	1000	.     
+1	145277108	145277572	LSU-rRNA_Hsa	1000	.     
+1	149033183	149035829	Satellite_repeat	1000	.     
+1	156186169	156186712	High_Mappability_island	1000	.     
+1	224199390	224204260	Satellite_repeat	1000	.     
+1	233318467	233318516	(CATTC)n	1000	.     
+1	236260366	236260821	Low_mappability_island	1000	.     
+1	237766308	237766764	LSU-rRNA_Hsa	1000	.     
+1	238105345	238105511	Low_mappability_island	1000	.     
+1	238108025	238108378	Low_mappability_island	1000	.     
+1	238108645	238109697	Low_mappability_island	1000	.     
+10	18841533	18862467	(CATTC)n	1000	.     
+10	20035661	20037171	Low_mappability_island	1000	.     
+10	36722282	36723650	Low_mappability_island	1000	.     
+10	38772277	38819357	Satellite_repeat	1000	.     
+10	38868892	38889025	Satellite_repeat	1000	.     
+10	39076515	39155771	Satellite_repeat	1000	.     
+10	42354835	42548642	centromeric_repeat	1000	.     
+10	42596676	42602082	Satellite_repeat	1000	.     
+10	42596700	42602110	Satellite_repeat	1000	.     
+10	42661264	42667623	Satellite_repeat	1000	.     
+10	42790522	42818398	Satellite_repeat	1000	.     
+10	135498649	135502716	Satellite_repeat	1000	.     
+11	6831669	6831838	ALR/Alpha	1000	.     
+11	10529403	10531969	Low_mappability_island	1000	.     
+11	48671444	48902406	centromeric_repeat	1000	.     
+11	48931242	48964015	centromeric_repeat	1000	.     
+11	50318471	50784078	centromeric_repeat	1000	.     
+11	51090700	51374066	centromeric_repeat	1000	.     
+11	51567242	51594226	centromeric_repeat	1000	.     
+11	54694046	55027975	centromeric_repeat	1000	.     
+11	73221660	73221946	Low_mappability_island	1000	.     
+11	85194913	85195322	LSU-rRNA_Hsa	1000	.     
+11	87524468	87525005	Low_mappability_island	1000	.     
+11	103275584	103281729	Low_mappability_island	1000	.     
+11	122874287	122874443	Low_mappability_island	1000	.     
+12	20704285	20704583	SSU-rRNA_Hsa	1000	.     
+12	34372315	34372825	LSU-rRNA_Hsa	1000	.     
+12	34432130	34857010	centromeric_repeat	1000	.     
+12	37989447	38441828	centromeric_repeat	1000	.     
+12	38531376	38531930	LSU-rRNA_Hsa	1000	.     
+12	41757383	41757545	Low_mappability_island	1000	.     
+12	127650407	127651075	LSU-rRNA_Hsa	1000	.     
+12	132061320	132062046	Low_mappability_island	1000	.     
+13	56545728	56545925	Low_mappability_island	1000	.     
+13	110076444	110076782	Low_mappability_island	1000	.     
+14	18999935	19056900	centromeric_repeat	1000	.     
+14	32953263	32954381	Low_mappability_island	1000	.     
+14	84637832	84639038	Low_mappability_island	1000	.     
+14	90341302	90341516	SSU-rRNA_Hsa	1000	.     
+15	19999941	20044132	centromeric_repeat	1000	.     
+16	32493036	32570826	ALR/Alpha	1000	.     
+16	32590063	32598801	ALR/Alpha	1000	.     
+16	33237130	33241330	Low_mappability_island	1000	.     
+16	33864355	34023306	centromeric_repeat	1000	.     
+16	34180542	34197081	Satellite_repeat	1000	.     
+16	34530115	34542632	BSR/Beta	1000	.     
+16	35193580	35285885	centromeric_repeat	1000	.     
+16	46385718	46456668	Satellite_repeat	1000	.     
+16	46497639	46500515	Satellite_repeat	1000	.     
+16	47538629	47539297	LSU-rRNA_Hsa	1000	.     
+17	19355538	19356096	LSU-rRNA_Hsa	1000	.     
+17	19502495	19506773	Low_mappability_island	1000	.     
+17	21905167	21906712	centromeric_repeat	1000	.     
+17	22018524	22032049	Low_mappability_island	1000	.     
+17	22221073	22263006	centromeric_repeat	1000	.     
+17	25263010	25268059	Satellite_repeat	1000	.     
+17	25415551	25417559	telomeric_repeat	1000	.     
+17	31149365	31149981	High_Mappability_island	1000	.     
+17	33478114	33478372	LSU-rRNA_Hsa	1000	.     
+17	41381502	41382591	High_Mappability_island	1000	.     
+17	41463538	41464075	High_Mappability_island	1000	.     
+17	41464478	41465015	snRNA	1000	.     
+17	41465562	41467288	High_Mappability_island	1000	.     
+17	51183038	51183763	Low_mappability_island	1000	.     
+17	55868618	55868752	LSU-rRNA_Hsa	1000	.     
+17	75158031	75158430	LSU-rRNA_Hsa	1000	.     
+18	96416	97552	Satellite_repeat	1000	.     
+18	105658	112233	Satellite_repeat	1000	.     
+18	2842252	2842356	Low_mappability_island	1000	.     
+18	15393801	15393992	centromeric_repeat	1000	.     
+18	18510894	18520356	centromeric_repeat	1000	.     
+18	44126235	44126593	(CATTC)n	1000	.     
+18	45379603	45379864	Low_mappability_island	1000	.     
+18	50319086	50319301	Low_mappability_island	1000	.     
+18	77772846	77773065	LSU-rRNA_Hsa	1000	.     
+19	246006	247844	TAR1	1000	.     
+19	22877614	22877696	SSU-rRNA_Hsa	1000	.     
+19	23235030	23235504	BSR/Beta	1000	.     
+19	24182398	24186210	LSU-rRNA_Hsa	1000	.     
+19	24385474	24633168	centromeric_repeat	1000	.     
+19	27730611	28262682	centromeric_repeat	1000	.     
+19	36066445	36066810	LSU-rRNA_Hsa	1000	.     
+19	36756398	36800948	centromeric_repeat	1000	.     
+19	37759473	37797722	centromeric_repeat	1000	.     
+19	44914313	44916340	ACRO1	1000	.     
+19	44960681	44962681	ACRO1	1000	.     
+2	739925	740994	Low_mappability_island	1000	.     
+2	49456729	49457067	Low_mappability_island	1000	.     
+2	88124390	88124903	Low_mappability_island	1000	.     
+2	89830421	89880514	Satellite_repeat	1000	.     
+2	90371401	90394776	Satellite_repeat	1000	.     
+2	90443001	90545431	Low_mappability_island	1000	.     
+2	91595080	91616015	Satellite_repeat	1000	.     
+2	92267428	92326280	centromeric_repeat	1000	.     
+2	115695017	115695281	LSU-rRNA_Hsa	1000	.     
+2	117781085	117781300	Low_mappability_island	1000	.     
+2	132966248	132989300	centromeric_repeat	1000	.     
+2	132994855	133007983	ALR/Alpha	1000	.     
+2	133011824	133013298	SSU-rRNA_Hsa	1000	.     
+2	133036250	133040042	LSU-rRNA_Hsa	1000	.     
+2	133044095	133045945	ACRO1	1000	.     
+2	143848503	143848792	Low_mappability_island	1000	.     
+2	148022736	148022878	Low_mappability_island	1000	.     
+2	149639207	149639515	Low_mappability_island	1000	.     
+2	156120500	156120610	Low_mappability_island	1000	.     
+2	162135000	162139241	Low_mappability_island	1000	.     
+2	230045426	230045796	LSU-rRNA_Hsa	1000	.     
+20	26257032	26320267	centromeric_repeat	1000	.     
+20	29517710	29521147	centromeric_repeat	1000	.     
+20	29803876	29833334	centromeric_repeat	1000	.     
+20	55932703	55936114	chrM	1000	.     
+20	62916702	62918053	telomeric_repeat	1000	.     
+21	9647205	9648529	Low_mappability_island	1000	.     
+21	9694896	9704962	centromeric_repeat	1000	.     
+21	9825451	9827612	High_Mappability_island	1000	.     
+21	9827612	9845233	Low_mappability_island	1000	.     
+21	9881895	9882569	TAR1	1000	.     
+21	10084922	10088004	Satellite_repeat	1000	.     
+21	10492876	10493049	Low_mappability_island	1000	.     
+21	10599428	10599915	TAR1	1000	.     
+21	10697886	10860890	centromeric_repeat	1000	.     
+21	11186054	11188131	Satellite_repeat	1000	.     
+21	14338127	14369791	centromeric_repeat	1000	.     
+21	18800575	18800997	(GAGTG)n	1000	.     
+21	27228003	27228242	SSU-rRNA_Hsa	1000	.     
+21	46796081	46796336	Low_mappability_island	1000	.     
+22	16847814	16862659	Satellite_repeat	1000	.     
+22	18876789	18884510	Satellite_repeat	1000	.     
+3	25508897	25509131	Low_mappability_island	1000	.     
+3	73159606	73161131	snRNA	1000	.     
+3	75696297	75699304	BSR/Beta	1000	.     
+3	75717841	75720426	Satellite_repeat	1000	.     
+3	80995858	81014459	ALR/Alpha	1000	.     
+3	90311686	90507410	centromeric_repeat	1000	.     
+3	93504815	93519133	centromeric_repeat	1000	.     
+3	96335934	96337436	Low_mappability_island	1000	.     
+3	160665423	160665642	Low_mappability_island	1000	.     
+3	196625514	196625860	Satellite_repeat	1000	.     
+3	197825427	197834080	Low_mappability_island	1000	.     
+4	9987	12694	telomeric_repeat	1000	.     
+4	12276463	12292424	ALR/Alpha	1000	.     
+4	12641862	12642305	Low_mappability_island	1000	.     
+4	21583630	21583719	(GAATG)n	1000	.     
+4	27732004	27732240	Low_mappability_island	1000	.     
+4	47774268	47774416	Low_mappability_island	1000	.     
+4	49085372	49342114	centromeric_repeat	1000	.     
+4	49488472	49662085	centromeric_repeat	1000	.     
+4	52659961	52688986	centromeric_repeat	1000	.     
+4	56194229	56194584	Low_mappability_island	1000	.     
+4	65473858	65473941	Low_mappability_island	1000	.     
+4	68264186	68266830	centromeric_repeat	1000	.     
+4	70296565	70296841	LSU-rRNA_Hsa	1000	.     
+4	76807083	76807320	LSU-rRNA_Hsa	1000	.     
+4	78929660	78929920	Low_mappability_island	1000	.     
+4	156374749	156377226	chrM	1000	.     
+4	156384860	156387314	Low_mappability_island	1000	.     
+4	163342479	163342744	Low_mappability_island	1000	.     
+4	190190746	190203442	Low_mappability_island	1000	.     
+4	190801869	190802909	Low_mappability_island	1000	.     
+4	190943802	190943962	Satellite_repeat	1000	.     
+4	190987268	190990949	Satellite_repeat	1000	.     
+4	191026302	191044344	telomeric_repeat	1000	.     
+5	17517177	17600940	Low_mappability_island	1000	.     
+5	21477365	21497415	Low_mappability_island	1000	.     
+5	34177882	34197574	Low_mappability_island	1000	.     
+5	45908253	46411114	centromeric_repeat	1000	.     
+5	49405493	49554574	centromeric_repeat	1000	.     
+5	71146650	71146996	LSU-rRNA_Hsa	1000	.     
+5	79945807	79948223	Low_mappability_island	1000	.     
+5	93903068	93906726	Low_mappability_island	1000	.     
+5	97746525	97746679	Low_mappability_island	1000	.     
+5	99381556	99390873	Low_mappability_island	1000	.     
+5	105889063	105889263	chrM	1000	.     
+5	123095972	123097432	chrM	1000	.     
+5	134258949	134264271	Low_mappability_island	1000	.     
+5	174541634	174542177	SSU-rRNA_Hsa	1000	.     
+6	58735349	58739031	centromeric_repeat	1000	.     
+6	58745955	58780547	centromeric_repeat	1000	.     
+6	61880095	61944008	centromeric_repeat	1000	.     
+6	62189892	62206612	ALR/Alpha	1000	.     
+6	62207809	62230644	ALR/Alpha	1000	.     
+6	62283966	62284581	Low_mappability_island	1000	.     
+6	133593944	133594201	LSU-rRNA_Hsa	1000	.     
+6	137059142	137059326	SSU-rRNA_Hsa	1000	.     
+6	150665074	150665281	SSU-rRNA_Hsa	1000	.     
+6	157731310	157735525	Low_mappability_island	1000	.     
+7	43878355	43878530	TAR1	1000	.     
+7	45291517	45291740	Low_mappability_island	1000	.     
+7	56437808	56442977	Low_mappability_island	1000	.     
+7	57253980	57254183	Low_mappability_island	1000	.     
+7	57255310	57255444	Low_mappability_island	1000	.     
+7	57261829	57261998	Low_mappability_island	1000	.     
+7	57544726	57556913	Satellite_repeat	1000	.     
+7	57811488	57836990	centromeric_repeat	1000	.     
+7	57939184	58055539	centromeric_repeat	1000	.     
+7	61054285	62454680	centromeric_repeat	1000	.     
+7	64059157	64066183	BSR/Beta	1000	.     
+7	64951348	64956223	centromeric_repeat	1000	.     
+7	68201468	68201673	Low_mappability_island	1000	.     
+7	68527370	68527788	LSU-rRNA_Hsa	1000	.     
+7	80962907	80963147	SSU-rRNA_Hsa	1000	.     
+7	100550640	100551321	Low_mappability_island	1000	.     
+7	142372972	142375638	Low_mappability_island	1000	.     
+7	145694403	145694561	Low_mappability_island	1000	.     
+8	155512	157639	TAR1	1000	.     
+8	21455971	21456306	LSU-rRNA_Hsa	1000	.     
+8	32868966	32873279	Low_mappability_island	1000	.     
+8	43092737	43097573	Satellite_repeat	1000	.     
+8	43399486	43843604	centromeric_repeat	1000	.     
+8	46838215	47457541	centromeric_repeat	1000	.     
+8	47739043	47742797	Low_mappability_island	1000	.     
+8	47750844	47776101	BSR/Beta	1000	.     
+8	56754955	56755418	LSU-rRNA_Hsa	1000	.     
+8	69218401	69218922	LSU-rRNA_Hsa	1000	.     
+8	70602248	70602620	LSU-rRNA_Hsa	1000	.     
+8	77114154	77114389	Low_mappability_island	1000	.     
+8	100508010	100508287	Low_mappability_island	1000	.     
+9	10435	11574	TAR1	1000	.     
+9	4799734	4800000	SSU-rRNA_Hsa	1000	.     
+9	33656606	33659249	Low_mappability_island	1000	.     
+9	42819021	42832395	centromeric_repeat	1000	.     
+9	44070617	44070871	Low_mappability_island	1000	.     
+9	44873123	44902307	centromeric_repeat	1000	.     
+9	45355954	45357644	telomeric_repeat	1000	.     
+9	45435109	45443517	centromeric_repeat	1000	.     
+9	66494170	66494805	TAR1	1000	.     
+9	66767710	66864329	centromeric_repeat	1000	.     
+9	66970914	67005594	centromeric_repeat	1000	.     
+9	67315122	67321036	centromeric_repeat	1000	.     
+9	67789868	67792893	centromeric_repeat	1000	.     
+9	68410775	68435115	Low_mappability_island	1000	.     
+9	69677073	69687998	centromeric_repeat	1000	.     
+9	69689770	69711497	centromeric_repeat	1000	.     
+9	69947961	70011196	centromeric_repeat	1000	.     
+9	70076144	70076855	centromeric_repeat	1000	.     
+9	70318723	70327683	centromeric_repeat	1000	.     
+9	72653073	72653572	Satellite_repeat	1000	.     
+9	78790077	78790255	(GAATG)n	1000	.     
+9	79186574	79187026	LSU-rRNA_Hsa	1000	.     
+9	141019938	141021783	TAR1	1000	.     
+MT	1	16569	chrM	1000	.     
+X	55206111	55206740	Low_mappability_island	1000	.     
+X	55207753	55208152	Low_mappability_island	1000	.     
+X	55208300	55208643	Low_mappability_island	1000	.     
+X	55208980	55209208	Low_mappability_island	1000	.     
+X	55209655	55210006	Low_mappability_island	1000	.     
+X	58330488	58330843	centromeric_repeat	1000	.     
+X	58373806	58373962	centromeric_repeat	1000	.     
+X	58377680	58377864	centromeric_repeat	1000	.     
+X	58415350	58416387	centromeric_repeat	1000	.     
+X	58432411	58432680	centromeric_repeat	1000	.     
+X	58485887	58486241	centromeric_repeat	1000	.     
+X	58488898	58494528	centromeric_repeat	1000	.     
+X	58499466	58504235	centromeric_repeat	1000	.     
+X	58506076	58528214	centromeric_repeat	1000	.     
+X	58528184	58536883	centromeric_repeat	1000	.     
+X	58544061	58582415	centromeric_repeat	1000	.     
+X	61681834	61919683	centromeric_repeat	1000	.     
+X	62003205	62041580	centromeric_repeat	1000	.     
+X	83658929	83659019	Low_mappability_island	1000	.     
+X	108297348	108297886	LSU-rRNA_Hsa	1000	.     
+X	114959057	115006437	Low_mappability_island	1000	.     
+X	125605623	125607351	Low_mappability_island	1000	.     
+X	125714985	125715338	Low_mappability_island	1000	.     
+X	125864844	125864980	Low_mappability_island	1000	.     
+X	125865719	125865874	Low_mappability_island	1000	.     
+Y	313470	313613	ALR/Alpha	1000	.     
+Y	3004989	3005175	LSU-rRNA_Hsa	1000	.     
+Y	4212807	4212910	Low_mappability_island	1000	.     
+Y	7671817	7694928	BSR/Beta	1000	.     
+Y	7726064	7730229	BSR/Beta	1000	.     
+Y	7730734	7731598	BSR/Beta	1000	.     
+Y	7735811	7752887	BSR/Beta	1000	.     
+Y	7785067	7806311	BSR/Beta	1000	.     
+Y	7806856	7814704	BSR/Beta	1000	.     
+Y	7815230	7820478	BSR/Beta	1000	.     
+Y	7829937	7832032	BSR/Beta	1000	.     
+Y	7832744	7848695	BSR/Beta	1000	.     
+Y	7870343	7873582	BSR/Beta	1000	.     
+Y	7874115	7874584	BSR/Beta	1000	.     
+Y	7875409	7885257	BSR/Beta	1000	.     
+Y	7886545	7894591	BSR/Beta	1000	.     
+Y	7898927	7916812	BSR/Beta	1000	.     
+Y	7918790	7921352	BSR/Beta	1000	.     
+Y	7926344	7936705	BSR/Beta	1000	.     
+Y	7941130	7947438	BSR/Beta	1000	.     
+Y	7948790	7964448	BSR/Beta	1000	.     
+Y	8179010	8181143	BSR/Beta	1000	.     
+Y	8181757	8213330	BSR/Beta	1000	.     
+Y	8214629	8215637	BSR/Beta	1000	.     
+Y	8220421	8230061	BSR/Beta	1000	.     
+Y	8230686	8231546	BSR/Beta	1000	.     
+Y	8240772	8265916	BSR/Beta	1000	.     
+Y	8291535	8292942	BSR/Beta	1000	.     
+Y	8294002	8295175	BSR/Beta	1000	.     
+Y	8296944	8321375	BSR/Beta	1000	.     
+Y	8325813	8325929	BSR/Beta	1000	.     
+Y	8326678	8333466	BSR/Beta	1000	.     
+Y	8334027	8342387	BSR/Beta	1000	.     
+Y	8356544	8369346	BSR/Beta	1000	.     
+Y	8909560	8909925	TAR1	1000	.     
+Y	8979478	8979585	Low_mappability_island	1000	.     
+Y	9072781	9072993	TAR1	1000	.     
+Y	9908430	9925608	centromeric_repeat	1000	.     
+Y	9981952	9982126	BSR/Beta	1000	.     
+Y	10034864	10036712	SSU-rRNA_Hsa	1000	.     
+Y	10040627	10045657	ALR/Alpha	1000	.     
+Y	10047773	10052533	ALR/Alpha	1000	.     
+Y	10053695	10057722	ALR/Alpha	1000	.     
+Y	10059394	10073694	ALR/Alpha	1000	.     
+Y	10075082	10075781	ALR/Alpha	1000	.     
+Y	10080736	10104539	ALR/Alpha	1000	.     
+Y	13104530	13144368	centromeric_repeat	1000	.     
+Y	13193966	13196535	Low_mappability_island	1000	.     
+Y	13252193	13259484	centromeric_repeat	1000	.     
+Y	13290177	13290667	chrM	1000	.     
+Y	13445957	13490591	Satellite_repeat	1000	.     
+Y	13642186	13749784	Satellite_repeat	1000	.     
+Y	13798522	13870984	Satellite_repeat	1000	.     
+Y	19691913	19692524	LSU-rRNA_Hsa	1000	.     
+Y	19764063	19776198	ALR/Alpha	1000	.     
+Y	19780600	19781704	ALR/Alpha	1000	.     
+Y	19783669	19796396	ALR/Alpha	1000	.     
+Y	19800068	19801419	ALR/Alpha	1000	.     
+Y	19808085	19817100	ALR/Alpha	1000	.     
+Y	19944298	19944581	TAR1	1000	.     
+Y	20235195	20235478	TAR1	1000	.     
+Y	20362679	20371694	ALR/Alpha	1000	.     
+Y	20378360	20379711	ALR/Alpha	1000	.     
+Y	20383383	20396110	ALR/Alpha	1000	.     
+Y	20398075	20399179	ALR/Alpha	1000	.     
+Y	20403581	20415713	ALR/Alpha	1000	.     
+Y	20487248	20487859	LSU-rRNA_Hsa	1000	.     
+Y	23124788	23125577	BSR/Beta	1000	.     
+Y	23149027	23151205	BSR/Beta	1000	.     
+Y	23157969	23158245	BSR/Beta	1000	.     
+Y	23159001	23167737	BSR/Beta	1000	.     
+Y	23178886	23181770	BSR/Beta	1000	.     
+Y	23220740	23223625	BSR/Beta	1000	.     
+Y	23234125	23235822	BSR/Beta	1000	.     
+Y	23236898	23248080	BSR/Beta	1000	.     
+Y	23248729	23248851	BSR/Beta	1000	.     
+Y	23899295	23899388	TAR1	1000	.     
+Y	23956449	23956628	TAR1	1000	.     
+Y	24247659	24247700	TAR1	1000	.     
+Y	24630999	24631040	TAR1	1000	.     
+Y	24953159	24975657	BSR/Beta	1000	.     
+Y	24980997	24991235	BSR/Beta	1000	.     
+Y	25022753	25039185	BSR/Beta	1000	.     
+Y	25040153	25042421	BSR/Beta	1000	.     
+Y	25048332	25059258	BSR/Beta	1000	.     
+Y	25060235	25064798	BSR/Beta	1000	.     
+Y	25099139	25121882	BSR/Beta	1000	.     
+Y	25122419	25160800	BSR/Beta	1000	.     
+Y	25182404	25192372	BSR/Beta	1000	.     
+Y	25217722	25219409	BSR/Beta	1000	.     
+Y	25493588	25495275	BSR/Beta	1000	.     
+Y	26148315	26148450	TAR1	1000	.     
+Y	26586905	26609405	BSR/Beta	1000	.     
+Y	26614745	26624983	BSR/Beta	1000	.     
+Y	26656502	26672934	BSR/Beta	1000	.     
+Y	26673902	26676170	BSR/Beta	1000	.     
+Y	26682081	26693007	BSR/Beta	1000	.     
+Y	26693984	26698547	BSR/Beta	1000	.     
+Y	26732883	26755623	BSR/Beta	1000	.     
+Y	26756160	26794538	BSR/Beta	1000	.     
+Y	26816148	26826116	BSR/Beta	1000	.     
+Y	26851466	26853153	BSR/Beta	1000	.     
+Y	27109247	27110934	BSR/Beta	1000	.     
+Y	27136281	27146249	BSR/Beta	1000	.     
+Y	27167859	27206241	BSR/Beta	1000	.     
+Y	27206778	27229502	BSR/Beta	1000	.     
+Y	27263848	27268411	BSR/Beta	1000	.     
+Y	27269388	27280315	BSR/Beta	1000	.     
+Y	27286226	27288494	BSR/Beta	1000	.     
+Y	27289462	27305895	BSR/Beta	1000	.     
+Y	27337415	27347656	BSR/Beta	1000	.     
+Y	27352996	27375497	BSR/Beta	1000	.     
+Y	27813984	27814119	TAR1	1000	.     
+Y	28555026	28555353	TAR1	1000	.     
+Y	28784129	28819695	Satellite_repeat	1000	.     
+Y	58819367	58917648	(CATTC)n	1000	.     
+Y	58971913	58997782	(CATTC)n	1000	.     
+Y	59361267	59362785	TAR1	1000	.     
\ No newline at end of file
diff --git a/assets/email_template.html b/assets/email_template.html
index de00e08c..e5f5f518 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -1,113 +1,53 @@
 <html>
-  <head>
-    <meta charset="utf-8" />
-    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
 
-    <meta
-      name="description"
-      content="nf-core/cutandrun: Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis."
-    />
-    <title>nf-core/cutandrun Pipeline Report</title>
-  </head>
-  <body>
-    <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
-      <img src="cid:nfcorepipelinelogo" />
+  <meta name="description" content="nf-core/cutandrun: Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.">
+  <title>nf-core/cutandrun Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-      <h1>nf-core/cutandrun v${version}</h1>
-      <h2>Run Name: $runName</h2>
+<img src="cid:nfcorepipelinelogo">
 
-      <% if (!success){ out << """
-      <div
-        style="
-          color: #a94442;
-          background-color: #f2dede;
-          border-color: #ebccd1;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
-        <h4 style="margin-top: 0; color: inherit">nf-core/cutandrun execution completed unsuccessfully!</h4>
+<h1>nf-core/cutandrun v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/cutandrun execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
-        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
-      </div>
-      """ } else { out << """
-      <div
-        style="
-          color: #3c763d;
-          background-color: #dff0d8;
-          border-color: #d6e9c6;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+    </div>
+    """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
         nf-core/cutandrun execution completed successfully!
-      </div>
-      """ } %>
+    </div>
+    """
+}
+%>
 
-      <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-      <p>The command used to launch the workflow was as follows:</p>
-      <pre
-        style="
-          white-space: pre-wrap;
-          overflow: visible;
-          background-color: #ededed;
-          padding: 15px;
-          border-radius: 4px;
-          margin-bottom: 30px;
-        "
-      >
-$commandLine</pre
-      >
+<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+<p>The command used to launch the workflow was as follows:</p>
+<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
 
-      <h3>Pipeline Configuration:</h3>
-      <table
-        style="
-          width: 100%;
-          max-width: 100%;
-          border-spacing: 0;
-          border-collapse: collapse;
-          border: 0;
-          margin-bottom: 30px;
-        "
-      >
-        <tbody style="border-bottom: 1px solid #ddd">
-          <% out << summary.collect{ k,v -> "
-          <tr>
-            <th
-              style="
-                text-align: left;
-                padding: 8px 0;
-                line-height: 1.42857143;
-                vertical-align: top;
-                border-top: 1px solid #ddd;
-              "
-            >
-              $k
-            </th>
-            <td
-              style="
-                text-align: left;
-                padding: 8px;
-                line-height: 1.42857143;
-                vertical-align: top;
-                border-top: 1px solid #ddd;
-              "
-            >
-              <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
-            </td>
-          </tr>
-          " }.join("\n") %>
-        </tbody>
-      </table>
+<h3>Pipeline Configuration:</h3>
+<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
+    <tbody style="border-bottom: 1px solid #ddd;">
+        <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
+    </tbody>
+</table>
 
-      <p>nf-core/cutandrun</p>
-      <p><a href="https://github.com/nf-core/cutandrun">https://github.com/nf-core/cutandrun</a></p>
-    </div>
-  </body>
-</html>
+<p>nf-core/cutandrun</p>
+<p><a href="https://github.com/nf-core/cutandrun">https://github.com/nf-core/cutandrun</a></p>
+
+</div>
+
+</body>
+</html>
\ No newline at end of file
diff --git a/assets/email_template.txt b/assets/email_template.txt
index d34cf2af..3d4bd78f 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -6,7 +6,6 @@
                                         `._,._,'
   nf-core/cutandrun v${version}
 ----------------------------------------------------
-
 Run Name: $runName
 
 <% if (success){
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
new file mode 100644
index 00000000..47dbc791
--- /dev/null
+++ b/assets/methods_description_template.yml
@@ -0,0 +1,25 @@
+id: "nf-core-cutandrun-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/cutandrun Methods Description"
+section_href: "https://github.com/nf-core/cutandrun"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using nf-core/cutandrun v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
+  <pre><code>${workflow.commandLine}</code></pre>
+  <h4>References</h4>
+  <ul>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>
diff --git a/assets/multiqc/frip_score_header.txt b/assets/multiqc/frip_score_header.txt
new file mode 100644
index 00000000..a0cab909
--- /dev/null
+++ b/assets/multiqc/frip_score_header.txt
@@ -0,0 +1,17 @@
+#id: 'primary_frip_score'
+#parent_id: 'peak_qc'
+#parent_name: 'Peak QC'
+#parent_description: 'This section contains peak-based QC reports'
+#section_name: 'Sample FRiP score'
+#description: "is generated by calculating the fraction of all mapped fragments that fall
+#              into the peak regions called by either MACS2 or SEACR.
+#              See <a href='https://www.encodeproject.org/data-standards/terms/' target='_blank'>FRiP score</a>."
+#plot_type: 'bargraph'
+#anchor: 'primary_fripscore'
+#pconfig:
+#    id: 'primary_fripscore_plot'
+#    title: 'FRiP score'
+#    ylab: 'FRiP score'
+#    ymax: 1
+#    ymin: 0
+#    tt_decimals: 2
diff --git a/assets/multiqc/peak_counts_consensus_header.txt b/assets/multiqc/peak_counts_consensus_header.txt
new file mode 100644
index 00000000..0423cafd
--- /dev/null
+++ b/assets/multiqc/peak_counts_consensus_header.txt
@@ -0,0 +1,13 @@
+#id: 'consensus_peak_counts'
+#parent_id: 'peak_qc'
+#parent_name: 'Peak QC'
+#parent_description: 'This section contains peak-based QC reports'
+#section_name: 'Consensus Peak Count'
+#description: 'Calculated from the total number of peaks called by MACS2 or SEACR'
+#plot_type: 'bargraph'
+#anchor: 'consensus_peakcounts'
+#pconfig:
+#    id: 'consensus_peakcounts_plot'
+#    title: 'Total Peak Counts'
+#    ylab: "# Peaks"
+#    cpswitch_counts_label: 'Number of Peaks'
diff --git a/assets/multiqc/peak_counts_header.txt b/assets/multiqc/peak_counts_header.txt
new file mode 100644
index 00000000..c6145c8a
--- /dev/null
+++ b/assets/multiqc/peak_counts_header.txt
@@ -0,0 +1,13 @@
+#id: 'primary_peak_counts'
+#parent_id: 'peak_qc'
+#parent_name: 'Peak QC'
+#parent_description: 'This section contains peak-based QC reports'
+#section_name: 'Sample Peak Count'
+#description: 'Calculated from the total number of peaks called by MACS2 or SEACR'
+#plot_type: 'bargraph'
+#anchor: 'primary_peakcounts'
+#pconfig:
+#    id: 'primary_peakcounts_plot'
+#    title: 'Total Peak Counts'
+#    ylab: "# Peaks"
+#    cpswitch_counts_label: 'Number of Peaks'
diff --git a/assets/multiqc/peak_reprod_header.txt b/assets/multiqc/peak_reprod_header.txt
new file mode 100644
index 00000000..daccd629
--- /dev/null
+++ b/assets/multiqc/peak_reprod_header.txt
@@ -0,0 +1,13 @@
+#id: 'peak_reprod_perc'
+#parent_id: 'peak_qc'
+#parent_name: 'Peak QC'
+#parent_description: 'This section contains peak-based QC reports'
+#section_name: 'Sample Peak reproducibility %'
+#description: 'Calculated from the total number of overlapping peaks within group replicate sets'
+#plot_type: 'bargraph'
+#anchor: 'primary_peakrepro'
+#pconfig:
+#    id: 'primary_peakrepro_plot'
+#    title: 'Peak reproducibility %'
+#    ylab: "Reprod Fraction"
+#    stacking: None
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 982e93ee..bfba9bd4 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -2,17 +2,9 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/cutandrun" target="_blank">nf-core/cutandrun</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/cutandrun" target="_blank">documentation</a>.
-report_section_order:
-  software_versions:
-    order: -1000
-  nf-core-cutandrun-summary:
-    order: -1001
 
 export_plots: true
 
-report_header_info:
-  - Application Type: "CUT&RUN"
-
 # Run only these modules
 run_modules:
   - custom_content
@@ -20,7 +12,9 @@ run_modules:
   - cutadapt
   - bowtie2
   - samtools
+  - preseq
   - picard
+  - deeptools
 
 module_order:
   - fastqc:
@@ -42,26 +36,52 @@ module_order:
       name: "Bowtie2 (spike-in)"
       path_filters:
         - "./bowtie2_spikein/*.bowtie2.log"
-  - samtools
-  - picard
+  - samtools:
+      name: "Samtools alignment scores"
+  - preseq:
+      name: "Library Complexity"
+  - picard:
+      name: "Picard duplication stats"
+  - deeptools:
+      name: "Fragment QC"
   - custom_content
 
+report_section_order:
+  fragment_lengths:
+    order: -1001
+  peak_qc:
+    order: -1002
+  software_versions:
+    order: -1003
+  nf-core-cutandrun-summary:
+    order: -1004
+
 custom_content:
   order:
-    - fragment_lengths
-    - software_versions
-    - software_versions_unique
-extra_fn_clean_exts:
-  - "_val_1"
-  - "_val_2"
+    - primary_peak_counts
+    - consensus_peak_counts
+    - primary_frip_score
+    - peak_reprod_perc
+    - software-versions-by-process
+    - software-versions-unique
+
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible:
-  FastQC:
+  fastqc:
     percent_duplicates: False
 
+extra_fn_clean_trim:
+  - ".spikein"
+  - ".target"
+  - ".target.filtered"
+  - "_1"
+  - "_2"
+  - "_1_val_1"
+  - "_2_val_2"
+
 section_comments:
   fastqc_raw_fastqc_per_base_sequence_content: >
-    The discordant sequence content at the begining of the reads are common phenomenon for CUT&TAG reads. Failing to pass the Per base seuqnence content does not mean your data failed.
+    Discordant sequence content at the beginning of the reads are common phenomenon for CUT&TAG/RUN reads. Failing to pass the Per-base sequence content does not mean your data failed.
     - It can be due to the Tn5 preference.
     - What you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling. In any case we do not recommend trimming as the bowtie2 parameters that we list will give accurate mapping information without trimming.
 
diff --git a/bin/calc_frag_hist.py b/bin/calc_frag_hist.py
new file mode 100755
index 00000000..24a3614a
--- /dev/null
+++ b/bin/calc_frag_hist.py
@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+
+import os
+import glob
+import argparse
+
+import numpy as np
+import pandas as pd
+
+############################################
+############################################
+## PARSE ARGUMENTS
+############################################
+############################################
+Description = "Calclate fragment histogram"
+
+parser = argparse.ArgumentParser(description=Description)
+
+## REQUIRED PARAMETERS
+parser.add_argument("--frag_path")
+parser.add_argument("--output")
+args = parser.parse_args()
+
+############################################
+############################################
+## MAIN FUNCTION
+############################################
+############################################
+
+print("Calclate fragment histogram")
+
+# Init
+frag_path = os.path.abspath(args.frag_path)
+frag_hist = None
+
+# Create list of deeptools raw fragment files
+dt_frag_list = glob.glob(frag_path)
+dt_frag_list.sort()
+
+for i in list(range(len(dt_frag_list))):
+    # Create dataframe from csv file for each file and save to a list of data frames
+    dt_frag_i = pd.read_csv(dt_frag_list[i], sep="\t", header=None, names=["Size", "Occurrences"])
+    frag_base_i = os.path.basename(dt_frag_list[i])
+
+    # Split txt file paths on dots
+    sample_id_list = frag_base_i.split(".")
+
+    # Join list on the elements of the sample id
+    separator = ""
+    sample_id = separator.join(sample_id_list[0:-2])
+
+    # Split sample id on underscores
+    sample_id_split_list = sample_id.split("_")
+
+    # Take first element of this list for group id
+    group_i = separator.join(sample_id_split_list[0:-1])
+
+    # Take last element of this list for replicate number
+    rep_i = sample_id_split_list[-1]
+
+    # Round column and convert occurrences to int
+    dt_frag_i = dt_frag_i.round(1)
+    dt_frag_i = dt_frag_i.astype(int)
+
+    # Create long forms of fragment histograms
+    dt_frag_i_long = np.repeat(dt_frag_i["Size"].values, dt_frag_i["Occurrences"].values)
+    dt_group_i_long = np.repeat(group_i, len(dt_frag_i_long))
+    dt_rep_i_long = np.repeat(rep_i, len(dt_frag_i_long))
+
+    dt_group_i_short = np.repeat(group_i, dt_frag_i.shape[0])
+    dt_rep_i_short = np.repeat(rep_i, dt_frag_i.shape[0])
+
+    if i == 0:
+        frags_arr = dt_frag_i_long
+        group_arr = dt_group_i_long
+        rep_arr = dt_rep_i_long
+
+        group_short = dt_group_i_short
+        rep_short = dt_rep_i_short
+        frag_hist = dt_frag_i
+    else:
+        frags_arr = np.append(frags_arr, dt_frag_i_long)
+        group_arr = np.append(group_arr, dt_group_i_long)
+        rep_arr = np.append(rep_arr, dt_rep_i_long)
+
+        group_short = np.append(group_short, dt_group_i_short)
+        rep_short = np.append(rep_short, dt_rep_i_short)
+        frag_hist = frag_hist.append(dt_frag_i)
+
+frag_hist["group"] = group_short
+frag_hist["replicate"] = rep_short
+frag_hist = frag_hist.reset_index(drop=True)
+
+size_list = frag_hist["Size"].to_numpy().astype(str)
+occurrences_list = frag_hist["Occurrences"].to_numpy().astype(str)
+size_list_sep = np.core.defchararray.add(size_list, " : ")
+x_y_list = np.core.defchararray.add(size_list_sep, occurrences_list)
+
+group_rep = frag_hist[["group", "replicate"]].groupby(["group", "replicate"]).size().reset_index()
+first_line = "data:"
+
+for i in list(range(group_rep.shape[0])):
+    group_i = group_rep.at[i, "group"]
+    rep_i = group_rep.at[i, "replicate"]
+    str_list = x_y_list[(frag_hist["group"] == group_i) & (frag_hist["replicate"] == rep_i)]
+
+    x_y_str = ", ".join(str_list)
+    full_line_i = "    '" + group_i + "_" + rep_i + "' : {" + x_y_str + "}"
+    if i == 0:
+        frag_len_hist_mqc_dict = "\n".join([first_line, full_line_i])
+
+    else:
+        frag_len_hist_mqc_dict = "\n".join([frag_len_hist_mqc_dict, full_line_i])
+
+txt_mqc = open(args.output, "w")
+txt_mqc.write(frag_len_hist_mqc_dict)
+txt_mqc.close()
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index db042cde..7d38ce17 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -13,7 +13,10 @@ def parse_args(args=None):
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
     parser.add_argument("FILE_IN", help="Input samplesheet file.")
     parser.add_argument("FILE_OUT", help="Output file.")
-    parser.add_argument("USE_CONTROL", help="Boolean for whether or not the user has specified the pipeline must normalise against a control")
+    parser.add_argument(
+        "USE_CONTROL",
+        help="Boolean for whether or not the user has specified the pipeline must normalise against a control",
+    )
     return parser.parse_args(args)
 
 
@@ -45,16 +48,16 @@ def check_samplesheet(file_in, file_out, use_control):
     WT,1,WT_LIB2_REP1_1.fastq.gz,WT_LIB2_REP1_2.fastq.gz,CONTROL_GROUP
     WT,2,WT_LIB1_REP2_1.fastq.gz,WT_LIB1_REP2_2.fastq.gz,CONTROL_GROUP
     KO,1,KO_LIB1_REP1_1.fastq.gz,KO_LIB1_REP1_2.fastq.gz,CONTROL_GROUP
-    CONTROL_GROUP,1,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz, 
-    CONTROL_GROUP,2,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz, 
+    CONTROL_GROUP,1,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz,
+    CONTROL_GROUP,2,KO_LIB1_REP1_1.fastq.gz,IGG_LIB1_REP1_2.fastq.gz,
     """
 
     # Init
     control_present = False
-    num_fastq_list     = []
-    sample_names_list  = []
+    num_fastq_list = []
+    sample_names_list = []
     control_names_list = []
-    sample_run_dict    = {}
+    sample_run_dict = {}
 
     with open(file_in, "r") as fin:
 
@@ -66,7 +69,11 @@ def check_samplesheet(file_in, file_out, use_control):
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
 
         if len(header) >= len(LEGACY_HEADER) and header[: len(LEGACY_HEADER)] == LEGACY_HEADER:
-            print("ERROR: It looks like you are using a legacy header format with a newer version of the pipeline -> {} != {}".format(",".join(header), ",".join(HEADER)))
+            print(
+                "ERROR: It looks like you are using a legacy header format with a newer version of the pipeline -> {} != {}".format(
+                    ",".join(header), ",".join(HEADER)
+                )
+            )
             sys.exit(1)
 
         if header[: len(HEADER)] != HEADER:
@@ -74,21 +81,28 @@ def check_samplesheet(file_in, file_out, use_control):
             sys.exit(1)
 
         ## Check sample entries
+        line_no = 1
         for line in fin:
             lspl = [x.strip().strip('"') for x in line.strip().split(",")]
 
-            ## Set control_present to true if the control column is not empty
-            if lspl[4] != "":
-                control_present = True
+            ## Check if its just a blank line so we dont error
+            if line.strip() == "":
+                continue
 
             ## Check valid number of columns per row
             if len(lspl) != HEADER_LEN:
                 print_error(
-                    "Invalid number of columns (found {} should be {})!".format(len(lspl), len(HEADER)),
+                    "Invalid number of columns (found {} should be {})! - line no. {}".format(
+                        len(lspl), len(HEADER), line_no
+                    ),
                     "Line",
                     line,
                 )
 
+            ## Set control_present to true if the control column is not empty
+            if lspl[4] != "":
+                control_present = True
+
             ## Check valid number of populated columns per row
             num_cols = len([x for x in lspl if x])
             if num_cols < MIN_COLS:
@@ -154,7 +168,7 @@ def check_samplesheet(file_in, file_out, use_control):
                     print_error("Samplesheet contains duplicate rows!", "Line", line)
                 else:
                     sample_run_dict[sample][replicate].append(sample_info)
-            
+
             ## Store unique sample names
             if sample not in sample_names_list:
                 sample_names_list.append(sample)
@@ -163,6 +177,8 @@ def check_samplesheet(file_in, file_out, use_control):
             if control not in control_names_list:
                 control_names_list.append(control)
 
+            line_no = line_no + 1
+
     ## Check data is either paired-end/single-end and not both
     if min(num_fastq_list) != max(num_fastq_list):
         print_error("Mixture of paired-end and single-end reads!")
@@ -170,7 +186,9 @@ def check_samplesheet(file_in, file_out, use_control):
     ## Check control group exists
     for ctrl in control_names_list:
         if ctrl != "" and ctrl not in sample_names_list:
-            print_error("Each control entry must match at least one group entry! Unmatched control entry: {}.".format(ctrl))
+            print_error(
+                "Each control entry must match at least one group entry! Unmatched control entry: {}.".format(ctrl)
+            )
 
     ## Create control identity variable
     for sample in sorted(sample_run_dict.keys()):
@@ -183,15 +201,21 @@ def check_samplesheet(file_in, file_out, use_control):
                             print_error("Control cannot have a control: {}.".format(sample_info[0]))
                     else:
                         sample_info.append("0")
-                else: 
+                else:
                     sample_info.append("0")
 
     ## Check use_control parameter is consistent with input groups
-    if (use_control == 'true' and not control_present):
-        print_error("ERROR: No 'control' group was found in " + str(file_in) + " If you are not supplying a control, please specify --use_control 'false' on command line.")
-        
-    if (use_control == 'false' and control_present):
-        print("WARNING: Parameter --use_control was set to false, but an control group was found in " + str(file_in) + ".")
+    if use_control == "true" and not control_present:
+        print_error(
+            "ERROR: No 'control' group was found in "
+            + str(file_in)
+            + " If you are not supplying a control, please specify --use_control 'false' on command line."
+        )
+
+    if use_control == "false" and control_present:
+        print(
+            "WARNING: Parameter --use_control was set to false, but an control group was found in " + str(file_in) + "."
+        )
 
     ## Write validated samplesheet with appropriate columns
     if len(sample_run_dict) > 0:
@@ -199,7 +223,10 @@ def check_samplesheet(file_in, file_out, use_control):
         make_dir(out_dir)
         with open(file_out, "w") as fout:
 
-            fout.write(",".join(["id", "group", "replicate", "control", "single_end", "fastq_1", "fastq_2", "is_control"]) + "\n")
+            fout.write(
+                ",".join(["id", "group", "replicate", "control", "single_end", "fastq_1", "fastq_2", "is_control"])
+                + "\n"
+            )
             for sample in sorted(sample_run_dict.keys()):
 
                 ## Check that replicate ids are in format 1..<NUM_REPS>
@@ -216,10 +243,7 @@ def check_samplesheet(file_in, file_out, use_control):
                     check_group = sample_run_dict[sample][replicate][0][2]
                     for tech_rep in sample_run_dict[sample][replicate]:
                         if tech_rep[2] != check_group:
-                            print_error(
-                                "Control group must match within technical replicates",
-                                tech_rep[2]
-                            )
+                            print_error("Control group must match within technical replicates", tech_rep[2])
 
                     ## Write to file
                     for idx, sample_info in enumerate(sample_run_dict[sample][replicate]):
@@ -231,5 +255,6 @@ def main(args=None):
     args = parse_args(args)
     check_samplesheet(args.FILE_IN, args.FILE_OUT, args.USE_CONTROL)
 
+
 if __name__ == "__main__":
-    sys.exit(main())
\ No newline at end of file
+    sys.exit(main())
diff --git a/bin/frip.py b/bin/frip.py
deleted file mode 100755
index f174d82f..00000000
--- a/bin/frip.py
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import glob
-import argparse
-
-import deeptools.countReadsPerBin as crpb
-import pysam
-
-############################################
-############################################
-## PARSE ARGUMENTS
-############################################
-############################################
-Description = 'Calclate FRIP scores (FRagment proportion in Peaks regions) using deeptools for each sample'
-
-parser = argparse.ArgumentParser(description=Description)
-
-## REQUIRED PARAMETERS
-parser.add_argument('--bams', help="Bam file.")
-parser.add_argument('--peaks', help="Peaks interval file.")
-parser.add_argument('--threads', help="the number of threads for the task.")
-parser.add_argument('--outpath', help="Full path to output directory.")
-args = parser.parse_args()
-
-############################################
-############################################
-## MAIN FUNCTION
-############################################
-############################################
-
-# https://deeptools.readthedocs.io/en/develop/content/example_api_tutorial.html
-
-# Create file lists
-bam_file_list = glob.glob(args.bams)
-peak_file_list = glob.glob(args.peaks)
-
-frips = []
-for idx, bam_file in enumerate(bam_file_list):
-    # Init
-    frip = 0
-
-    # Read first line
-    first_line = None
-    with open(peak_file_list[idx], "r") as file:
-        for line in file:
-            first_line = line
-            break
-
-    if first_line is not None:
-        print("Calculating " + bam_file + " using " + peak_file_list[idx])
-        cr = crpb.CountReadsPerBin([bam_file], bedFile=[peak_file_list[idx]], numberOfProcessors=int(1))
-
-        # Calc the total number of reads in peaks per bam file
-        reads_at_peaks = cr.run()
-        total = reads_at_peaks.sum(axis=0)
-
-        # Load up bam file and get the total number of mapped reads
-        bam = pysam.AlignmentFile(bam_file)
-
-        # Calc frip
-        frip = float(total[0]) / bam.mapped
-
-    frips.append(str(frip))
-
-    # Log
-    print("Frip = " + str(frip))
-
-# Create string and write to file
-frip_string = ",".join(frips)
-writer = open(os.path.join(args.outpath, "frips.csv"), "w")
-writer.write("frip\n")
-writer.write(frip_string)
-writer.close()
diff --git a/bin/gtf2bed b/bin/gtf2bed
new file mode 100755
index 00000000..0163049e
--- /dev/null
+++ b/bin/gtf2bed
@@ -0,0 +1,131 @@
+#!/usr/bin/env perl
+
+# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
+
+use Getopt::Long;
+
+my $extended;
+my $displaynames = '';
+GetOptions("x"=>\$extended, "names"=>\$displaynames);
+
+$in = shift @ARGV;
+
+my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n";
+open IN, $in_cmd;
+
+while (<IN>) {
+    $gff = 2 if /^##gff-version 2/;
+    $gff = 3 if /^##gff-version 3/;
+    next if /^#/ && $gff;
+
+    s/\s+$//;
+    # 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
+    my @f = split /\t/;
+    if ($gff) {
+        # most ver 2's stick gene names in the id field
+        ($id) = $f[8]=~ /\bID="([^"]+)"/;
+        # most ver 3's stick unquoted names in the name field
+        ($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
+    } else {
+        ($id) = $f[8]=~ /transcript_id "([^"]+)"/;
+    }
+
+    next unless $id && $f[0];
+
+    if ($f[2] eq 'exon') {
+        die "no position at exon on line $." if ! $f[3];
+        # gff3 puts :\d in exons sometimes
+        $id =~ s/:\d+$// if $gff == 3;
+        push @{$exons{$id}}, \@f;
+        # save lowest start
+        $trans{$id} = \@f if !$trans{$id};
+    } elsif ($f[2] eq 'start_codon') {
+        #optional, output codon start/stop as "thick" region in bed
+        $sc{$id}->[0] = $f[3];
+    } elsif ($f[2] eq 'stop_codon') {
+        $sc{$id}->[1] = $f[4];
+    } elsif ($f[2] eq 'miRNA' ) {
+        $trans{$id} = \@f if !$trans{$id};
+        push @{$exons{$id}}, \@f;
+    }
+}
+
+for $id (
+    # sort by chr then pos
+    sort {
+        $trans{$a}->[0] eq $trans{$b}->[0] ?
+        $trans{$a}->[3] <=> $trans{$b}->[3] :
+        $trans{$a}->[0] cmp $trans{$b}->[0]
+    } (keys(%trans)) ) {
+        my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
+        my ($cds, $cde);
+        ($cds, $cde) = @{$sc{$id}} if $sc{$id};
+
+        # sort by pos
+        my @ex = sort {
+            $a->[3] <=> $b->[3]
+        } @{$exons{$id}};
+
+        my $beg = $ex[0][3];
+        my $end = $ex[-1][4];
+
+        if ($dir eq '-') {
+            # swap
+            $tmp=$cds;
+            $cds=$cde;
+            $cde=$tmp;
+            $cds -= 2 if $cds;
+            $cde += 2 if $cde;
+        }
+
+        # not specified, just use exons
+        $cds = $beg if !$cds;
+        $cde = $end if !$cde;
+
+        # adjust start for bed
+        --$beg; --$cds;
+
+        my $exn = @ex;												# exon count
+        my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
+        my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
+
+        my $gene_id;
+        my $extend = "";
+
+        ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+        ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+        if ($extended) {
+            $extend="\t$gene_id";
+        }
+
+        if ($displaynames) {
+            print "$chr\t$beg\t$end\t$gene_id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+        } else {
+            print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+        }
+
+        # added an extra comma to make it look exactly like ucsc's beds
+        # print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+}
+
+close IN;
diff --git a/bin/igv_files_to_session.py b/bin/igv_files_to_session.py
index cf7c3124..7ed47df0 100755
--- a/bin/igv_files_to_session.py
+++ b/bin/igv_files_to_session.py
@@ -22,12 +22,24 @@
 argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
 
 ## REQUIRED PARAMETERS
-argParser.add_argument('XML_OUT', help="XML output file.")
-argParser.add_argument('LIST_FILE', help="Tab-delimited file containing two columns i.e. file_name\tcolour. Header isnt required.")
-argParser.add_argument('GENOME', help="Full path to genome fasta file or shorthand for genome available in IGV e.g. hg19.")
+argParser.add_argument("XML_OUT", help="XML output file.")
+argParser.add_argument(
+    "LIST_FILE", help="Tab-delimited file containing two columns i.e. file_name\tcolour. Header isnt required."
+)
+argParser.add_argument(
+    "GENOME", help="Full path to genome fasta file or shorthand for genome available in IGV e.g. hg19."
+)
+argParser.add_argument("GTF_BED")
 
 ## OPTIONAL PARAMETERS
-argParser.add_argument('-pp', '--path_prefix', type=str, dest="PATH_PREFIX", default='', help="Path prefix to be added at beginning of all files in input list file.")
+argParser.add_argument(
+    "-pp",
+    "--path_prefix",
+    type=str,
+    dest="PATH_PREFIX",
+    default="",
+    help="Path prefix to be added at beginning of all files in input list file.",
+)
 args = argParser.parse_args()
 
 ############################################
@@ -36,6 +48,7 @@
 ############################################
 ############################################
 
+
 def makedir(path):
 
     if not len(path) == 0:
@@ -45,80 +58,125 @@ def makedir(path):
             if exception.errno != errno.EEXIST:
                 raise
 
+
 ############################################
 ############################################
 ## MAIN FUNCTION
 ############################################
 ############################################
 
-def igv_files_to_session(XMLOut,ListFile,Genome,PathPrefix=''):
+
+def igv_files_to_session(XMLOut, ListFile, Genome, GtfBed, PathPrefix=""):
 
     makedir(os.path.dirname(XMLOut))
 
     fileList = []
-    fin = open(ListFile,'r')
+    fin = open(ListFile, "r")
     while True:
         line = fin.readline()
         if line:
-            ifile,colour = line.strip().split('\t')
+            ifile, colour = line.strip().split("\t")
             if len(colour.strip()) == 0:
-                colour = '0,0,178'
-            fileList.append((PathPrefix.strip()+ifile,colour))
+                colour = "0,0,178"
+            fileList.append((PathPrefix.strip() + ifile, colour))
         else:
             break
             fout.close()
 
     ## ADD RESOURCES SECTION
-    XMLStr =  '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
+    XMLStr = '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
     XMLStr += '<Session genome="%s" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">\n' % (Genome)
-    XMLStr += '\t<Resources>\n'
-    for ifile,colour in fileList:
+    XMLStr += "\t<Resources>\n"
+    for ifile, colour in fileList:
         XMLStr += '\t\t<Resource path="%s"/>\n' % (ifile)
-    XMLStr += '\t</Resources>\n'
+    XMLStr += '\t\t<Resource path="./%s"/>\n' % (GtfBed)
+    XMLStr += "\t</Resources>\n"
 
-    ## ADD PANEL SECTION
     XMLStr += '\t<Panel height="1160" name="DataPanel" width="1897">\n'
-    for ifile,colour in fileList:
+
+    # Render gene file first
+    XMLStr += (
+        '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,48,73" '
+    )
+    XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
+    XMLStr += (
+        'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n'
+        % (GtfBed, os.path.basename(GtfBed))
+    )
+
+    ## Do a GTF pass first
+    for ifile, colour in fileList:
+        extension = os.path.splitext(ifile)[1].lower()
+        if extension in [".gtf"]:
+            XMLStr += (
+                '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" '
+                % (colour)
+            )
+            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
+            XMLStr += (
+                'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n'
+                % (ifile, os.path.basename(ifile))
+            )
+        elif extension in [".gff"]:
+            XMLStr += (
+                '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" '
+                % (colour)
+            )
+            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
+            XMLStr += (
+                'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n'
+                % (ifile, os.path.basename(ifile))
+            )
+
+    ## Then beds/narrowpeak
+    for ifile, colour in fileList:
         extension = os.path.splitext(ifile)[1].lower()
-        if extension in ['.bed','.broadpeak','.narrowpeak']:
-            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
+        if extension in [".bed", ".broadpeak", ".narrowpeak"]:
+            XMLStr += (
+                '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" '
+                % (colour)
+            )
             XMLStr += 'displayMode="SQUISHED" featureVisibilityWindow="-1" fontSize="12" height="20" '
-            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
-        elif extension in ['.bw', '.bigwig', '.tdf']:
-            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="true" clazz="org.broad.igv.track.DataSourceTrack" color="%s" ' % (colour)
+            XMLStr += (
+                'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n'
+                % (ifile, os.path.basename(ifile))
+            )
+        elif extension in [".bw", ".bigwig", ".tdf", ".bedGraph", ".bedgraph"]:
+            XMLStr += (
+                '\t\t<Track altColor="0,0,178" autoScale="true" clazz="org.broad.igv.track.DataSourceTrack" color="%s" '
+                % (colour)
+            )
             XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" height="100" '
-            XMLStr += 'id="%s" name="%s" normalize="false" renderer="BAR_CHART" sortable="true" visible="true" windowFunction="mean">\n' % (ifile,os.path.basename(ifile))
+            XMLStr += (
+                'id="%s" name="%s" normalize="false" renderer="BAR_CHART" sortable="true" visible="true" windowFunction="mean">\n'
+                % (ifile, os.path.basename(ifile))
+            )
             XMLStr += '\t\t\t<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10" minimum="0.0" type="LINEAR"/>\n'
-            XMLStr += '\t\t</Track>\n'
-        elif extension in ['.gtf']:
-            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
-            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
-            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
-        elif extension in ['.gff']:
-            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
-            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" '
-            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
-        elif extension in ['.bam']:
+            XMLStr += "\t\t</Track>\n"
+        elif extension in [".bam"]:
             pass
-        else:
-            XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
-            XMLStr += 'displayMode="SQUISHED" featureVisibilityWindow="-1" fontSize="10" height="20" '
-            XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
-
-    XMLStr += '\t</Panel>\n'
-    #XMLStr += '\t<HiddenAttributes>\n\t\t<Attribute name="DATA FILE"/>\n\t\t<Attribute name="DATA TYPE"/>\n\t\t<Attribute name="NAME"/>\n\t</HiddenAttributes>\n'
-    XMLStr += '</Session>'
-    XMLOut = open(XMLOut,'w')
+        # else:
+        #     XMLStr += '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" ' % (colour)
+        #     XMLStr += 'displayMode="SQUISHED" featureVisibilityWindow="-1" fontSize="10" height="20" '
+        #     XMLStr += 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n' % (ifile,os.path.basename(ifile))
+
+    XMLStr += "\t</Panel>\n"
+    # XMLStr += '\t<HiddenAttributes>\n\t\t<Attribute name="DATA FILE"/>\n\t\t<Attribute name="DATA TYPE"/>\n\t\t<Attribute name="NAME"/>\n\t</HiddenAttributes>\n'
+    XMLStr += "</Session>"
+    XMLOut = open(XMLOut, "w")
     XMLOut.write(XMLStr)
     XMLOut.close()
 
+
 ############################################
 ############################################
 ## RUN FUNCTION
 ############################################
 ############################################
 
-igv_files_to_session(XMLOut=args.XML_OUT,ListFile=args.LIST_FILE,Genome=args.GENOME,PathPrefix=args.PATH_PREFIX)
+igv_files_to_session(
+    XMLOut=args.XML_OUT, ListFile=args.LIST_FILE, Genome=args.GENOME, GtfBed=args.GTF_BED, PathPrefix=args.PATH_PREFIX
+)
 
 ############################################
 ############################################
diff --git a/bin/lib/reports.py b/bin/lib/reports.py
deleted file mode 100644
index 43ff5f2e..00000000
--- a/bin/lib/reports.py
+++ /dev/null
@@ -1,588 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-import os
-import glob
-import numpy as np
-import pandas as pd
-import matplotlib.pyplot as plt
-from matplotlib.backends.backend_pdf import PdfPages
-from matplotlib.ticker import FuncFormatter
-import seaborn as sns
-
-class Reports:
-    metadata_table = None
-    frag_hist = None
-    frag_violin = None
-    frag_bin500 = None
-    seacr_beds = None
-    bams = None
-
-    def __init__(self, logger, meta, meta_ctrl, raw_frags, bin_frag, seacr_bed):
-        self.logger = logger
-        self.meta_path = meta
-        self.meta_ctrl_path = meta_ctrl
-        self.raw_frag_path = raw_frags
-        self.bin_frag_path = bin_frag
-        self.seacr_bed_path = seacr_bed
-
-        sns.set()
-        sns.set_theme()
-        sns.set_context("paper")
-
-    #*
-    #========================================================================================
-    # UTIL
-    #========================================================================================
-    #*/
-
-    def format_millions(self, x, pos):
-        #the two args are the value and tick position
-        return '%1.1fM' % (x * 1e-6)
-
-    def format_thousands(self, x, pos):
-        #the two args are the value and tick position
-        return '%1.1fK' % (x * 1e-3)
-
-    def gen_pdf(self, output_path, plots):
-        with PdfPages(os.path.join(output_path, 'merged_report.pdf')) as pdf:
-            for key in plots:
-                pdf.savefig(plots[key])
-
-    #*
-    #========================================================================================
-    # ENTRY POINTS
-    #========================================================================================
-    #*/
-
-    def generate_cutandrun_reports(self, output_path):
-        # Init
-        abs_path = os.path.abspath(output_path)
-
-        # Get plots and supporting data tables
-        plots, data, mqc_frag_hist = self.generate_reports()
-
-        # Save mqc text file
-        txt_mqc = open(os.path.join(abs_path, "03_03_frag_len_mqc.txt"), "w")
-        txt_mqc.write(mqc_frag_hist)
-        txt_mqc.close()
-
-        # Save data to output folder
-        for key in data:
-            data[key].to_csv(os.path.join(abs_path, key + '.csv'), index=False)
-
-        # Save plots to output folder
-        for key in plots:
-            plots[key].savefig(os.path.join(abs_path, key + '.png'))
-
-        # Save pdf of the plots
-        self.gen_pdf(abs_path, plots)
-
-    #*
-    #========================================================================================
-    # LOAD DATA
-    #========================================================================================
-    #*/
-
-    def load_meta_data(self):
-        # Plots supported
-
-        # Sequencing Depth
-        # Alignable Fragments
-        # Alignment Rate (Target)
-        # Alignment Rate (Spike-in)
-        # Duplication Rate
-        # Estimated Library Size
-        # Unique Fragments
-        # Spike-in Scale Factor
-        # Normalised Fragment Count
-
-        self.metadata_noctrl_table = pd.read_csv(self.meta_path, sep=',')
-        self.metadata_table = pd.read_csv(self.meta_ctrl_path, sep=',')
-
-        self.duplicate_info = False
-        if 'dedup_percent_duplication' in self.metadata_table.columns:
-            self.duplicate_info = True
-
-        self.scale_factor_info = False
-        if 'scale_factor' in self.metadata_table.columns:
-            self.scale_factor_info = True
-
-        # Make new perctenage alignment columns
-        self.metadata_table['target_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_target')] / self.metadata_table.loc[:, ('bt2_total_reads_target')] * 100
-        self.metadata_table['spikein_alignment_rate'] = self.metadata_table.loc[:, ('bt2_total_aligned_spikein')] / self.metadata_table.loc[:, ('bt2_total_reads_spikein')] * 100
-
-        # Change to percentage
-        if 'frip' in self.metadata_noctrl_table.columns:
-            self.metadata_noctrl_table['frip'] =  self.metadata_noctrl_table['frip'] * 100
-
-        # Sort tables
-        self.metadata_table = self.metadata_table.sort_values('group')
-        self.metadata_noctrl_table = self.metadata_noctrl_table.sort_values('group')
-
-    def load_raw_frag_histogram(self):
-        # Plots supported
-
-        # Fragment Length Distribution (the main frag length lineplot)
-        # Fragment Length Distribution (the main frag length violin plot)
-
-        # Create list of deeptools raw fragment files
-        dt_frag_list = glob.glob(self.raw_frag_path)
-        dt_frag_list.sort()
-
-        for i in list(range(len(dt_frag_list))):
-            # Create dataframe from csv file for each file and save to a list
-            dt_frag_i = pd.read_csv(dt_frag_list[i], sep='\t', header=None, names=['Size','Occurrences'])
-            frag_base_i = os.path.basename(dt_frag_list[i])
-
-            #  split txt files on dots
-            sample_id_list = frag_base_i.split(".")
-
-            # join list on the elements of the sample id
-            separator = ""
-            sample_id = separator.join(sample_id_list[0:-2])
-
-            # split sample id on underscores
-            sample_id_split_list = sample_id.split("_")
-
-            #  take first element of this list for group id
-            group_i = separator.join(sample_id_split_list[0:-1])
-
-            #  take last element of this list for replicate number
-            rep_i = sample_id_split_list[-1]
-
-            # Create long forms of fragment histograms
-            dt_frag_i_long = np.repeat(dt_frag_i['Size'].values, dt_frag_i['Occurrences'].values)
-            dt_group_i_long = np.repeat(group_i, len(dt_frag_i_long))
-            dt_rep_i_long = np.repeat(rep_i, len(dt_frag_i_long))
-
-            dt_group_i_short = np.repeat(group_i, dt_frag_i.shape[0])
-            dt_rep_i_short = np.repeat(rep_i, dt_frag_i.shape[0])
-
-            if i==0:
-                frags_arr = dt_frag_i_long
-                group_arr = dt_group_i_long
-                rep_arr = dt_rep_i_long
-
-                group_short = dt_group_i_short
-                rep_short = dt_rep_i_short
-                self.frag_hist = dt_frag_i
-            else:
-                frags_arr = np.append(frags_arr, dt_frag_i_long)
-                group_arr = np.append(group_arr, dt_group_i_long)
-                rep_arr = np.append(rep_arr, dt_rep_i_long)
-
-                group_short = np.append(group_short, dt_group_i_short)
-                rep_short = np.append(rep_short, dt_rep_i_short)
-                self.frag_hist = self.frag_hist.append(dt_frag_i)
-
-        self.frag_hist['group'] = group_short
-        self.frag_hist['replicate'] = rep_short
-        self.frag_hist = self.frag_hist.reset_index(drop=True)
-        self.frag_violin = pd.DataFrame( { "fragment_size" : frags_arr, "group" : group_arr , "replicate": rep_arr} )
-
-    def load_binned_frags(self):
-        # Plots supported
-
-        # Replicate Reproducibility
-
-        # Start by creating list of bin500 files
-        dt_bin_frag_list = glob.glob(self.bin_frag_path)
-        dt_bin_frag_list.sort()
-
-        for i in list(range(len(dt_bin_frag_list))):
-            dt_bin_frag_i_read = pd.read_csv(dt_bin_frag_list[i], sep='\t', header=None, names=['chrom','bin','count','sample'])
-            sample_name = dt_bin_frag_i_read['sample'].iloc[0].split(".")[0]
-            dt_bin_frag_i = dt_bin_frag_i_read[['chrom','bin','count']]
-            dt_bin_frag_i.columns = ['chrom','bin',sample_name]
-
-            if i==0:
-                self.frag_bin500 = dt_bin_frag_i
-
-            else:
-                self.frag_bin500 = pd.merge(self.frag_bin500, dt_bin_frag_i, on=['chrom','bin'], how='outer')
-
-        # Add log2 transformed count data column
-        # log2_counts = self.frag_bin500[self.frag_bin500.columns[-(len(dt_bin_frag_list)):]].transform(lambda x: np.log2(x))
-        # self.frag_bin500 = pd.concat([self.frag_bin500[['chrom','bin']],log2_counts], axis=1)
-
-        self.frag_bin500 = self.frag_bin500.fillna(0)
-
-    def load_seacr_peaks(self):
-        # Plots supported
-
-        # Total Peaks
-        # Peak Width
-
-        # Create dataframe for seacr peaks
-        seacr_bed_list = glob.glob(self.seacr_bed_path)
-
-        # combine all seacr bed files into one df including group and replicate info
-        for i in list(range(len(seacr_bed_list))):
-            seacr_bed_i = pd.read_csv(seacr_bed_list[i], sep='\t', header=None, usecols=[0,1,2,3,4], names=['chrom','start','end','total_signal','max_signal'])
-            bed_base_i = os.path.basename(seacr_bed_list[i])
-
-            #  split bed files on dots
-            bed_id_list = bed_base_i.split(".")
-
-            # join list on the elements of the sample id
-            separator = ""
-            sample_id = separator.join(bed_id_list[0:-4])
-
-            # split sample id on underscores
-            sample_id_split_list = sample_id.split("_")
-
-            #  take first element of this list for group id
-            group_i = separator.join(sample_id_split_list[0:-1])
-
-            # take last element fo this list for replicate number
-            rep_i = sample_id_split_list[-1]
-
-            seacr_bed_i['group'] = np.repeat(group_i, seacr_bed_i.shape[0])
-            seacr_bed_i['replicate'] = np.repeat(rep_i, seacr_bed_i.shape[0])
-
-            if i==0:
-                self.seacr_beds = seacr_bed_i
-
-            else:
-                self.seacr_beds = self.seacr_beds.append(seacr_bed_i)
-
-        # Get peak stats by group and replicate
-        self.seacr_beds_group_rep = self.seacr_beds[['group','replicate']].groupby(['group','replicate']).size().reset_index().rename(columns={0:'all_peaks'})
-
-    def load_data(self):
-        # ---------- Data - Load main meta-data table --------- #
-        self.load_meta_data()
-
-        # ---------- Data - Raw frag histogram --------- #
-        self.load_raw_frag_histogram()
-
-        # ---------- Data - Binned frags --------- #
-        self.load_binned_frags()
-
-        # ---------- Data - Peaks --------- #
-        self.load_seacr_peaks()
-
-    #*
-    #========================================================================================
-    # GEN REPORTS
-    #========================================================================================
-    #*/
-
-    def generate_reports(self):
-        # Init
-        plots = dict()
-        data = dict()
-
-        # Get Data
-        self.load_data()
-
-        # Plot section 1
-        multi_plot, data1 = self.alignment_summary()
-        plots["01_01_seq_depth"] = multi_plot[0]
-        plots["01_02_alignable_frag"] = multi_plot[1]
-        plots["01_03_alignment_rate_target"] = multi_plot[2]
-        plots["01_04_alignment_rate_spikein"] = multi_plot[3]
-        data["01_alignment_summary"] = data1
-
-        # Plot section 2
-        if self.duplicate_info == True:
-            multi_plot, data2 = self.duplication_summary()
-            plots["02_01_dup_rate"] = multi_plot[0]
-            plots["02_02_est_lib_size"] = multi_plot[1]
-            plots["02_03_unique_frags"] = multi_plot[2]
-            data["02_duplication_summary"] = data2
-
-        #  Plot 3
-        plot3, data3 = self.fraglen_summary_violin()
-        plots["03_01_frag_len_violin"] = plot3
-        data["03_01_frag_len_violin"] = data3
-
-        # Plot 4
-        plot4, data4 = self.fraglen_summary_histogram()
-        plots["03_02_frag_len_hist"] = plot4
-        data["03_02_frag_len_hist"] = data4
-
-        # Plot 5
-        plot5, data5 = self.replicate_heatmap()
-        plots["04_replicate_heatmap"] = plot5
-        data["04_replicate_heatmap"] = data5
-
-        # Plot section 6
-        if self.scale_factor_info == True:
-            multi_plot, data6 = self.scale_factor_summary()
-            plots["05_01_scale_factor"] = multi_plot[0]
-            plots["05_02_frag_count"] = multi_plot[1]
-            data["05_scale_factor_summary"] = data6
-
-        # Plot 7a
-        plot7a, data7a = self.no_of_peaks()
-        plots["06_01_no_of_peaks"] = plot7a
-        data["06_01_no_of_peaks"] = data7a
-
-        # Plot 7b
-        plot7b, data7b = self.peak_widths()
-        plots["06_02_peak_widths"] = plot7b
-        data["06_02_peak_widths"] = data7b
-
-        # Plot 7c
-        if 'peak_repro' in self.metadata_noctrl_table.columns:
-            plot7c, data7c = self.reproduced_peaks()
-            plots["06_03_reproduced_peaks"] = plot7c
-            data["06_03_reproduced_peaks"] = data7c
-
-        # Plot 7d
-        if 'frip' in self.metadata_noctrl_table.columns:
-            plot7d, data7d = self.frags_in_peaks()
-            plots["06_04_frags_in_peaks"] = plot7d
-            data["06_04_frags_in_peaks"] = data7d
-
-        # Fragment Length Histogram data in MultiQC yaml format
-        mqc_frag_hist = self.frag_len_hist_mqc()
-
-        return (plots, data, mqc_frag_hist)
-
-    #*
-    #========================================================================================
-    # TXT FILES
-    #========================================================================================
-    #*/
-
-    def frag_len_hist_mqc(self):
-        size_list = self.frag_hist["Size"].to_numpy().astype(str)
-        occurrences_list = self.frag_hist["Occurrences"].to_numpy().astype(str)
-        size_list_sep = np.core.defchararray.add(size_list, " : ")
-        x_y_list = np.core.defchararray.add(size_list_sep, occurrences_list)
-
-        group_rep = self.frag_hist[['group','replicate']].groupby(['group','replicate']).size().reset_index()
-        first_line = "data:"
-
-        for i in list(range(group_rep.shape[0])):
-            group_i = group_rep.at[i,"group"]
-            rep_i = group_rep.at[i,"replicate"]
-            str_list = x_y_list[ (self.frag_hist['group'] == group_i) & (self.frag_hist['replicate'] == rep_i) ]
-            # print(str_list)
-
-            x_y_str = ", ".join(str_list)
-            full_line_i = "    '" + group_i + "_" + rep_i + "' : {" + x_y_str + "}"
-            if i==0:
-                frag_len_hist_mqc_dict = "\n".join([first_line, full_line_i])
-
-            else:
-                frag_len_hist_mqc_dict = "\n".join([frag_len_hist_mqc_dict, full_line_i])
-
-
-        return frag_len_hist_mqc_dict
-
-    #*
-    #========================================================================================
-    # PLOTS
-    #========================================================================================
-    #*/
-
-    # ---------- Plot 1 - Alignment Summary --------- #
-    def alignment_summary(self):
-        sns.color_palette("magma", as_cmap=True)
-        sns.set(font_scale=0.6)
-        # Subset data
-        df_data = self.metadata_table.loc[:, ('id', 'group', 'bt2_total_reads_target', 'bt2_total_aligned_target', 'target_alignment_rate', 'spikein_alignment_rate')]
-
-        # Create plots array
-        figs = []
-
-        # Seq depth
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='bt2_total_reads_target', palette = "magma")
-        fig.suptitle("Sequencing Depth")
-        ax.set(ylabel="Total Reads")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # Alignable fragments
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='bt2_total_aligned_target', palette = "magma")
-        fig.suptitle("Alignable Fragments")
-        ax.set(ylabel="Total Aligned Reads")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # Alignment rate hg38
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='target_alignment_rate', palette = "magma")
-        fig.suptitle("Alignment Rate (Target)")
-        ax.set(ylabel="Percent of Fragments Aligned")
-        #ax.set(ylim=(0, 100))
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # Alignment rate e.coli
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='spikein_alignment_rate', palette = "magma")
-        fig.suptitle("Alignment Rate (Spike-in)")
-        ax.set(ylabel="Percent of Fragments Aligned")
-        #ax.set(ylim=(0, 100))
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        return figs, df_data
-
-    # ---------- Plot 2 - Duplication Summary --------- #
-    def duplication_summary(self):
-        # Init
-        k_formatter = FuncFormatter(self.format_thousands)
-        m_formatter = FuncFormatter(self.format_millions)
-
-        # Subset data
-        df_data = self.metadata_table.loc[:, ('id', 'group', 'dedup_percent_duplication', 'dedup_estimated_library_size', 'dedup_read_pairs_examined')]
-        df_data['dedup_percent_duplication'] *= 100
-        df_data['unique_frag_num'] = df_data['dedup_read_pairs_examined'] * (1-df_data['dedup_percent_duplication']/100)
-
-        # Create plots array
-        figs = []
-
-        # Duplication rate
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='dedup_percent_duplication', palette = "magma")
-        fig.suptitle("Duplication Rate")
-        ax.set(ylabel="Rate (%)")
-        ax.set(ylim=(0, 100))
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # Estimated library size
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='dedup_estimated_library_size', palette = "magma")
-        fig.suptitle("Estimated Library Size")
-        ax.set(ylabel="Size")
-        ax.yaxis.set_major_formatter(m_formatter)
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # No. of unique fragments
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data, x='group', y='unique_frag_num', palette = "magma")
-        fig.suptitle("Unique Fragments")
-        ax.set(ylabel="Count")
-        ax.yaxis.set_major_formatter(k_formatter)
-        ax.xaxis.set_tick_params(labelrotation=45)
-        ax.set(ylim=(0))
-        figs.append(fig)
-
-        return figs, df_data
-
-    # ---------- Plot 3 - Fragment Distribution Violin --------- #
-    def fraglen_summary_violin(self):
-        fig, ax = plt.subplots()
-        ax = sns.violinplot(data=self.frag_violin, x="group", y="fragment_size", hue="replicate", palette = "viridis")
-        ax.set(ylabel="Fragment Size")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        fig.suptitle("Fragment Length Distribution")
-
-        return fig, self.frag_violin
-
-    # ---------- Plot 4 - Fragment Distribution Histogram --------- #
-    def fraglen_summary_histogram(self):
-        fig, ax = plt.subplots()
-        ax = sns.lineplot(data=self.frag_hist, x="Size", y="Occurrences", hue="group", style="replicate", palette = "magma")
-        fig.suptitle("Fragment Length Distribution")
-
-        return fig, self.frag_hist
-
-    # ---------- Plot 5 - Replicate Reproducibility Heatmap --------- #
-    def replicate_heatmap(self):
-        fig, ax = plt.subplots()
-        plot_data = self.frag_bin500[self.frag_bin500.columns[-(len(self.frag_bin500.columns)-2):]]
-        # plot_data = plot_data.fillna(0)
-        corr_mat = plot_data.corr(method='pearson')
-        ax = sns.heatmap(corr_mat, annot=True, vmin=0, vmax=1)
-        fig.suptitle("Replicate Reproducibility (read counts in 500bp bins)")
-
-        return fig, self.frag_bin500
-
-    # ---------- Plot 6 - Scale Factor Comparison --------- #
-    def scale_factor_summary(self):
-        # Get normalised count data
-        df_normalised_frags = self.metadata_table.loc[:, ('id', 'group')]
-        df_normalised_frags['normalised_frags'] = self.metadata_table['bt2_total_reads_target']*self.metadata_table['scale_factor']
-
-        figs = []
-
-        # Subset meta data
-        df_data_scale = self.metadata_table.loc[:, ('id', 'group','scale_factor')]
-
-        # Scale factor
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_data_scale, x='group', y='scale_factor', palette = "magma")
-        fig.suptitle("Spike-in Scale Factor")
-        ax.set(ylabel="Coefficient")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        # Normalised fragment count
-        fig, ax = plt.subplots()
-        ax = sns.boxplot(data=df_normalised_frags, x='group', y='normalised_frags', palette = "magma")
-        fig.suptitle("Normalised Fragment Count")
-        ax.set(ylabel="Count")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        figs.append(fig)
-
-        return figs, df_data_scale
-
-    # ---------- Plot 7 - Peak Analysis --------- #
-    def no_of_peaks(self):
-    # 7a - Number of peaks
-        fig, ax = plt.subplots()
-        fig.suptitle("Total Peaks")
-
-        ax = sns.boxplot(data=self.seacr_beds_group_rep, x='group', y='all_peaks', palette = "magma")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        ax.set_ylabel("No. of Peaks")
-
-        return fig, self.seacr_beds_group_rep
-
-    # 7b - Width of peaks
-    def peak_widths(self):
-        fig, ax = plt.subplots()
-
-        ## add peak width column
-        self.seacr_beds['peak_width'] = self.seacr_beds['end'] - self.seacr_beds['start']
-        self.seacr_beds['peak_width'] = self.seacr_beds['peak_width'].abs().astype('float64')
-
-        ax = sns.violinplot(data=self.seacr_beds, x="group", y="peak_width", hue="replicate", palette = "viridis")
-        ax.xaxis.set_tick_params(labelrotation=45)
-        ax.set_ylabel("Peak Width")
-        fig.suptitle("Peak Width Distribution")
-
-        return fig, self.seacr_beds
-
-
-    # 7c - Peaks reproduced
-    def reproduced_peaks(self):
-        fig, ax = plt.subplots()
-
-        # Subset data
-        df_data = self.metadata_noctrl_table.loc[:, ('id', 'group', 'peak_repro')]
-
-        # plot
-        ax = sns.boxplot(data=df_data, x="group", y="peak_repro", palette = "magma")
-        ax.set_ylabel("Peaks Reproduced (%)")
-        ax.set(ylim=(0, 100))
-        ax.xaxis.set_tick_params(labelrotation=45)
-        fig.suptitle("Peak Reproducibility")
-
-        return fig, df_data
-
-    # 7d - Fragments within peaks
-    def frags_in_peaks(self):
-        fig, ax = plt.subplots()
-
-        # Subset data
-        df_data = self.metadata_noctrl_table.loc[:, ('id', 'group', 'frip')]
-
-        ax = sns.boxplot(data=df_data, x='group', y='frip', palette = "magma")
-        ax.set_ylabel("Fragments within Peaks (%)")
-        ax.set(ylim=(0, 100))
-        ax.xaxis.set_tick_params(labelrotation=45)
-        fig.suptitle("Aligned Fragments within Peaks")
-
-        return fig, df_data
diff --git a/bin/peak_reproducability.py b/bin/peak_reproducibility.py
similarity index 52%
rename from bin/peak_reproducability.py
rename to bin/peak_reproducibility.py
index 86d07a28..4ae15d43 100755
--- a/bin/peak_reproducability.py
+++ b/bin/peak_reproducibility.py
@@ -13,14 +13,15 @@
 ## PARSE ARGUMENTS
 ############################################
 ############################################
-Description = 'Calclate peak reproducability percentage for each sample'
+Description = "Calclate peak reproducibility percentage for each sample"
 
 parser = argparse.ArgumentParser(description=Description)
 
 ## REQUIRED PARAMETERS
-parser.add_argument('--intersect', help="Peaks intersect file.")
-parser.add_argument('--threads', help="the number of threads for the task.")
-parser.add_argument('--outpath', help="Full path to output directory.")
+parser.add_argument("--sample_id", help="Sample id.")
+parser.add_argument("--intersect", help="Peaks intersect file.")
+parser.add_argument("--threads", help="the number of threads for the task.")
+parser.add_argument("--outpath", help="Full path to output directory.")
 args = parser.parse_args()
 
 ############################################
@@ -29,12 +30,12 @@
 ############################################
 ############################################
 
-# Init
+# Init
 peak_perc = 0
 numfiles = 0
 num_columns = 0
 
-print('Reading file')
+print("Reading file")
 
 # Read first line
 first_line = None
@@ -44,36 +45,60 @@
         break
 
 if first_line is not None:
-    first_line_split = first_line.split('\t')
+    first_line_split = first_line.split("\t")
     num_columns = len(first_line_split)
     numfiles = 1
 
 if numfiles != 0:
-    print('Number of columns: ' + str(num_columns))
+    print("Number of columns: " + str(num_columns))
 
     ddf_inter = None
     if num_columns == 6:
         # Read file in using dask
-        ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','key','file_num','count'],
-            dtype={'chrom':str,'start':np.int64,'end':np.int64,'key':str, 'file_num':np.int32, 'count':np.int32})
-        numfiles = ddf_inter['file_num'].max().compute()
+        ddf_inter = dd.read_csv(
+            args.intersect,
+            sep="\t",
+            header=None,
+            names=["chrom", "start", "end", "key", "file_num", "count"],
+            dtype={
+                "chrom": str,
+                "start": np.int64,
+                "end": np.int64,
+                "key": str,
+                "file_num": np.int32,
+                "count": np.int32,
+            },
+        )
+        numfiles = ddf_inter["file_num"].max().compute()
 
     elif num_columns == 5:
         # Read file in using dask
-        ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','key','count'],
-            dtype={'chrom':str,'start':np.int64,'end':np.int64,'key':str, 'file_num':np.int32, 'count':np.int32})
+        ddf_inter = dd.read_csv(
+            args.intersect,
+            sep="\t",
+            header=None,
+            names=["chrom", "start", "end", "key", "count"],
+            dtype={
+                "chrom": str,
+                "start": np.int64,
+                "end": np.int64,
+                "key": str,
+                "file_num": np.int32,
+                "count": np.int32,
+            },
+        )
         numfiles = 1
     else:
-        print('Invalid file format detected')
+        print("Invalid file format detected")
         exit(1)
 
-    print('Number of files: ' + str(numfiles))
+    print("Number of files: " + str(numfiles))
 
     # Find total number of peaks
     ddf_inter_grouped = ddf_inter.groupby(by=["key"]).size()
     df_inter_grouped = ddf_inter_grouped.compute()
     total_peaks = len(df_inter_grouped.index)
-    print('Total peaks: ' + str(total_peaks))
+    print("Total peaks: " + str(total_peaks))
 
     if total_peaks > 0:
         # Filter for files which had an overlap and group by peak
@@ -81,21 +106,20 @@
         ddf_inter_grouped = ddf_inter_filt.groupby(by=["key"]).size()
         df_inter_grouped = ddf_inter_grouped.compute()
         df_inter_grouped = df_inter_grouped.reset_index()
-        df_inter_grouped = df_inter_grouped.rename({0: 'count'}, axis=1)
+        df_inter_grouped = df_inter_grouped.rename({0: "count"}, axis=1)
 
         # Filter for peaks which have full overlap
         df_inter_grouped_filter = df_inter_grouped[df_inter_grouped["count"] == numfiles]
         overlap_peaks = len(df_inter_grouped_filter.index)
-        print('Overlap peaks: ' + str(overlap_peaks))
+        print("Overlap peaks: " + str(overlap_peaks))
 
-        # Calc peak percentage
+        # Calc peak percentage
         peak_perc = (overlap_peaks / total_peaks) * 100
 else:
-    print('Empty file detected')
+    print("Empty file detected")
 
 # Create string and write to file
 output_string = str(peak_perc)
-writer = open(os.path.join(args.outpath, "peak_repro.csv"), "w")
-writer.write("peak_repro\n")
-writer.write(output_string)
+writer = open(os.path.join(args.outpath, args.sample_id + "_peak_repro.tsv"), "w")
+writer.write(args.sample_id + "\t" + output_string + "\n")
 writer.close()
diff --git a/bin/consensus_peaks.py b/bin/plot_consensus_peaks.py
similarity index 64%
rename from bin/consensus_peaks.py
rename to bin/plot_consensus_peaks.py
index 8aa943e2..072a1f8b 100755
--- a/bin/consensus_peaks.py
+++ b/bin/plot_consensus_peaks.py
@@ -13,14 +13,14 @@
 ## PARSE ARGUMENTS
 ############################################
 ############################################
-Description = 'Upset ven diagram of consensus peaks.'
+Description = "Upset venn diagram of consensus peaks."
 Epilog = """Example usage: python consensus_peaks.py <MERGED_INTERVAL_FILE> """
 
 parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
 
 ## REQUIRED PARAMETERS
-parser.add_argument('--peaks', help="Merged peaks interval file with replicate counts column.")
-parser.add_argument('--outpath', help="Full path to output directory.")
+parser.add_argument("--peaks", help="Merged peaks interval file with replicate counts column.")
+parser.add_argument("--outpath", help="Full path to output directory.")
 args = parser.parse_args()
 
 ############################################
@@ -33,32 +33,38 @@
 peak_file_list = glob.glob(args.peaks)
 
 if len(peak_file_list) > 10:
-    print('WARN: There are too many files to generate an upset plot, cancelling figure generation')
+    print("WARN: There are too many files to generate an upset plot, cancelling figure generation")
     exit(0)
 
 peak_df_list = list()
 for i in list(range(len(peak_file_list))):
-    peaks_i = pd.read_csv(peak_file_list[i], sep='\t', header=None, usecols=[0,1,2,8,9], names=['chrom','start','end','sample_reps','count'])
-    peaks_i['sample_reps'] = peaks_i['sample_reps'].replace(".peaks.bed.stringent.bed", "", regex=True)
+    peaks_i = pd.read_csv(
+        peak_file_list[i],
+        sep="\t",
+        header=None,
+        usecols=[0, 1, 2, 8, 9],
+        names=["chrom", "start", "end", "sample_reps", "count"],
+    )
+    peaks_i["sample_reps"] = peaks_i["sample_reps"].replace(".peaks.bed.stringent.bed", "", regex=True)
     peak_df_list.append(peaks_i)
-    reps2 = peaks_i[peaks_i["count"]>1]
+    reps2 = peaks_i[peaks_i["count"] > 1]
 
 # add sorted column to each dataframe, and make new condensed dataframe list
 summary_peak_df_list = list()
 for i in list(range(len(peak_df_list))):
     peaks_i = peak_df_list[i]
-    peaks_i['sorted_samples'] = ''
+    peaks_i["sorted_samples"] = ""
     rows_now = peaks_i.shape[0]
     for j in list(range(rows_now)):
-        sample_list = peaks_i.at[j,'sample_reps']
-        sample_array = np.unique(sample_list.split(','))
+        sample_list = peaks_i.at[j, "sample_reps"]
+        sample_array = np.unique(sample_list.split(","))
         sample_sorted = sorted(sample_array)
         sample_str = ",".join(sample_sorted)
-        peaks_i.at[j,'sorted_samples'] = sample_str
-    summary_peaks_i = peaks_i[['sorted_samples', 'count']].groupby(['sorted_samples'], as_index = False).sum()
+        peaks_i.at[j, "sorted_samples"] = sample_str
+    summary_peaks_i = peaks_i[["sorted_samples", "count"]].groupby(["sorted_samples"], as_index=False).sum()
     summary_peak_df_list.append(summary_peaks_i)
 
-# construct data in appropriate format for upsetplot, and plot
+# construct data in appropriate format for upsetplot, and plot
 for i in list(range(len(summary_peak_df_list))):
     df_i = summary_peak_df_list[i]
     # Get group name
@@ -68,11 +74,11 @@
     categories = df_i.shape[0]
     cat_list = []
     for j in list(range(categories)):
-        summary_sample = df_i.at[j,'sorted_samples'].split(',')
+        summary_sample = df_i.at[j, "sorted_samples"].split(",")
         cat_list.append(summary_sample)
 
     # Plot
-    peak_counts = upsetplot.from_memberships(cat_list, data = df_i['count'])
+    peak_counts = upsetplot.from_memberships(cat_list, data=df_i["count"])
     upsetplot.plot(peak_counts)
     plt.show()
     plt.savefig(os.path.join(args.outpath, file_name))
diff --git a/bin/reporting.py b/bin/reporting.py
deleted file mode 100755
index afce480c..00000000
--- a/bin/reporting.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-
-import argparse
-import logging
-
-from lib.reports import Reports
-
-def init_logger(app_name, log_file = None):
-    logger = logging.getLogger(app_name)
-    logger.setLevel(logging.DEBUG)
-    formatter = logging.Formatter('%(asctime)s:%(name)s:%(levelname)s - %(message)s')
-
-    if log_file:
-        fh = logging.FileHandler(log_file)
-        fh.setLevel(logging.DEBUG)
-        fh.setFormatter(formatter)
-        logger.addHandler(fh)
-
-    ch = logging.StreamHandler()
-    ch.setLevel(logging.INFO)
-    ch.setFormatter(formatter)
-    logger.addHandler(ch)
-
-    return logger
-
-def gen_png(parsed_args):
-    meta_path = parsed_args.meta
-    meta_ctrl_path = parsed_args.meta_ctrl
-    frag_path = parsed_args.raw_frag
-    output_path = parsed_args.output
-    logger = init_logger('gen_img', parsed_args.log)
-    bin_frag_path = parsed_args.bin_frag
-    seacr_bed_path = parsed_args.seacr_bed
-
-    logger.info('Generating plots to output folder')
-    report_gen = Reports(logger, meta_path, meta_ctrl_path, frag_path, bin_frag_path, seacr_bed_path)
-    report_gen.generate_cutandrun_reports(output_path)
-
-    logger.info('Completed')
-
-if __name__ == '__main__':
-    # Create command args
-    parser = argparse.ArgumentParser()
-    subparsers = parser.add_subparsers(help='sub-command help')
-
-    # Generate reporting function
-    parser_genimg = subparsers.add_parser('gen_reports')
-    parser_genimg.set_defaults(func=gen_png)
-    parser_genimg.add_argument('--log', required=False)
-    parser_genimg.add_argument('--meta', required=True)
-    parser_genimg.add_argument('--meta_ctrl', required=True)
-    parser_genimg.add_argument('--raw_frag', required=True)
-    parser_genimg.add_argument('--bin_frag', required=True)
-    parser_genimg.add_argument('--seacr_bed', required=True)
-    parser_genimg.add_argument('--output', required=True)
-
-    # Parse
-    parsed_args = parser.parse_args()
-
-    # Init logging
-    logger = init_logger('reporting', parsed_args.log)
-    logger.info("CUT&RUN Python Reporting")
-
-    print(parsed_args)
-
-    # Call functions
-    parsed_args.func(parsed_args)
diff --git a/bin/reports.py b/bin/reports.py
new file mode 100644
index 00000000..6a6e5877
--- /dev/null
+++ b/bin/reports.py
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+import argparse
+import logging
+import os
+import glob
+import pandas as pd
+
+# *
+# ========================================================================================
+# UTIL
+# ========================================================================================
+# */
+
+
+def init_logger(app_name, log_file=None):
+    logger = logging.getLogger(app_name)
+    logger.setLevel(logging.INFO)
+    formatter = logging.Formatter("%(asctime)s:%(name)s:%(levelname)s - %(message)s")
+
+    if log_file:
+        fh = logging.FileHandler(log_file)
+        fh.setLevel(logging.INFO)
+        fh.setFormatter(formatter)
+        logger.addHandler(fh)
+
+    ch = logging.StreamHandler()
+    ch.setLevel(logging.INFO)
+    ch.setFormatter(formatter)
+    logger.addHandler(ch)
+
+    return logger
+
+
+# *
+# ========================================================================================
+# MAIN
+# ========================================================================================
+# */
+
+# Input a collection of file tables from different samples and append the sample ids, then output one table
+def merge_samples(args):
+    # Init
+    metadata_path = os.path.abspath(args.metadata)
+
+    # Log
+    logger.info("merge_samples " + metadata_path)
+
+    # Get file list
+    file_list = glob.glob(metadata_path)
+    file_list.sort()
+
+    df_metadata = None
+    for idx, file in enumerate(file_list):
+        # Strip sample id and group name
+        sample_id = os.path.basename(file).replace(args.id_parse_string, "")
+        group_name = "_".join(sample_id.split("_")[:-1])
+
+        # Load table
+        df_newdata = pd.read_csv(file, sep=",")
+        df_newdata["id"] = sample_id
+        df_newdata["group"] = group_name
+        df_newdata = df_newdata.set_index("id")
+
+        if idx == 0:
+            df_metadata = df_newdata
+        else:
+            df_metadata = df_metadata.append(df_newdata)
+
+    df_metadata.to_csv(args.output, index=True, sep=",")
+
+
+if __name__ == "__main__":
+    # Create command args
+    parser = argparse.ArgumentParser()
+    subparsers = parser.add_subparsers(help="sub-command help")
+    subparsers.required = True
+
+    # Generate reporting function
+    newparser = subparsers.add_parser("merge_samples")
+    newparser.set_defaults(func=merge_samples)
+    newparser.add_argument("--log", required=False)
+    newparser.add_argument("--metadata", required=True)
+    newparser.add_argument("--id_parse_string", required=True)
+    newparser.add_argument("--output", required=True)
+
+    # Parse
+    parsed_args = parser.parse_args()
+
+    # Init logging
+    logger = init_logger("reporting", parsed_args.log)
+    logger.info("CUT&RUN Python Reporting")
+
+    # Call functions
+    parsed_args.func(parsed_args)
diff --git a/conf/base.config b/conf/base.config
index 6fb65804..8da75675 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -17,6 +17,17 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 
+    // Process-specific resource requirements
+    // NOTE - Please try and re-use the labels below as much as possible.
+    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
+    //        If possible, it would be nice to keep the same label naming convention when
+    //        adding in your local modules too.
+    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    withLabel:process_single {
+        cpus   = { check_max( 1                  , 'cpus'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+    }
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
diff --git a/conf/flowswitch.config b/conf/flowswitch.config
index 566ea296..f9226c29 100644
--- a/conf/flowswitch.config
+++ b/conf/flowswitch.config
@@ -13,7 +13,8 @@ params {
     run_trim_galore_fastqc = true
 
     run_alignment          = true
-    run_q_filter           = false
+    run_read_filter        = true
+    run_preseq             = true
     run_mark_dups          = true
     run_remove_dups        = true
 
@@ -21,9 +22,10 @@ params {
     run_consensus_all      = false
 
     run_reporting          = true
-    run_deep_tools         = true
+    run_deeptools_heatmaps = true
+    run_deeptools_qc       = true
+    run_peak_qc            = true
     run_multiqc            = true
-    run_peak_plotting      = true
     run_igv                = true
 }
 
@@ -31,16 +33,16 @@ params.callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.tr
 
 if(params.consensus_peak_mode == 'all') { params.run_consensus_all  = true  }
 
-if(params.minimum_alignment_q_score > 0)                  { params.run_q_filter      = true  }
-if(params.skip_removeduplicates || !params.run_mark_dups) { params.run_remove_dups   = false }
-if(!params.gene_bed || params.skip_heatmaps)              { params.run_deep_tools    = false }
-if(params.skip_multiqc)                                   { params.run_multiqc       = false }
-if(params.skip_upset_plots)                               { params.run_peak_plotting = false }
-if(params.skip_igv)                                       { params.run_igv           = false }
+if(params.skip_removeduplicates || !params.run_mark_dups) { params.run_remove_dups        = false }
+if(params.skip_preseq)                                    { params.run_preseq             = false }
+if(params.skip_heatmaps)                                  { params.run_deeptools_heatmaps = false }
+if(params.skip_dt_qc)                                     { params.run_deeptools_qc       = false }
+if(params.skip_peak_qc)                                   { params.run_peak_qc            = false }
+if(params.skip_igv)                                       { params.run_igv                = false }
 if(params.skip_reporting) {
     params.run_reporting     = false
+    params.run_preseq        = false
     params.run_multiqc       = false
-    params.run_peak_plotting = false
 }
 
 if(params.only_input) {
@@ -48,7 +50,8 @@ if(params.only_input) {
     params.run_cat_fastq          = false
     params.run_trim_galore_fastqc = false
     params.run_alignment          = false
-    params.run_q_filter           = false
+    params.run_read_filter        = false
+    params.run_preseq             = false
     params.run_mark_dups          = false
     params.run_remove_dups        = false
     params.run_peak_calling       = false
@@ -61,7 +64,8 @@ if(params.only_genome) {
     params.run_cat_fastq          = false
     params.run_trim_galore_fastqc = false
     params.run_alignment          = false
-    params.run_q_filter           = false
+    params.run_read_filter        = false
+    params.run_preseq             = false
     params.run_mark_dups          = false
     params.run_remove_dups        = false
     params.run_peak_calling       = false
@@ -72,7 +76,8 @@ if(params.only_genome) {
 if(params.only_preqc) {
     params.run_genome_prep  = false
     params.run_alignment    = false
-    params.run_q_filter     = false
+    params.run_read_filter  = false
+    params.run_preseq       = false
     params.run_mark_dups    = false
     params.run_remove_dups  = false
     params.run_peak_calling = false
@@ -81,7 +86,8 @@ if(params.only_preqc) {
 }
 
 if(params.only_alignment) {
-    params.run_q_filter     = false
+    params.run_read_filter  = false
+    params.run_preseq       = false
     params.run_mark_dups    = false
     params.run_remove_dups  = false
     params.run_peak_calling = false
@@ -99,3 +105,5 @@ if(params.only_peak_calling) {
     params.run_reporting = false
     params.run_multiqc   = true
 }
+
+if(params.skip_multiqc) { params.run_multiqc = false }
diff --git a/conf/modules.config b/conf/modules.config
index b5ca710c..e50e98f2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -56,19 +56,24 @@ if(params.run_input_check) {
 ========================================================================================
 */
 
-if (params.run_genome_prep) {
+if(params.run_genome_prep) {
     process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_.*' {
+            ext.args2 = '--no-same-owner'
+        }
+
         withName: '.*PREPARE_GENOME:GUNZIP_.*' {
             publishDir = [
-                path: { "${params.outdir}/00_genome" },
-                mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: params.save_reference
+                enabled: false
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_.*' {
-            ext.args2 = '--no-same-owner'
+        withName: '.*PREPARE_GENOME:TABIX_BGZIPTABIX' {
+            publishDir = [
+                path: { "${params.outdir}/00_genome/annotation" },
+                mode: "${params.publish_dir_mode}",
+                enabled: params.save_reference
+            ]
         }
 
         withName: '.*CHROMSIZES' {
@@ -97,6 +102,71 @@ if (params.run_genome_prep) {
                 enabled: params.save_reference
             ]
         }
+
+        withName: '.*PREPARE_GENOME:SAMTOOLS_FAIDX' {
+            publishDir = [
+                path: { "${params.outdir}/00_genome" },
+                mode: "${params.publish_dir_mode}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: params.save_reference
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT' {
+            ext.prefix = { "${meta.id}.sorted" }
+            publishDir = [
+                path: { "${params.outdir}/00_genome/annotation" },
+                mode: "${params.publish_dir_mode}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: params.save_reference
+            ]
+        }
+    }
+}
+
+if (params.run_genome_prep && params.blacklist) {
+    process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_AWK' {
+            ext.command = "'{OFS = \"\\t\"} {print \$1, '0', \$2}'"
+            ext.ext     = "bed"
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT' {
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT' {
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT' {
+            publishDir = [
+                path: { "${params.outdir}/00_genome" },
+                mode: "${params.publish_dir_mode}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: params.save_reference
+            ]
+        }
+    }
+}
+
+if (params.run_genome_prep && !params.gene_bed) {
+    process {
+        withName: '.*PREPARE_GENOME:GTF2BED' {
+            publishDir = [
+                path: { "${params.outdir}/00_genome/annotation" },
+                mode: "${params.publish_dir_mode}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: params.save_reference
+            ]
+        }
     }
 }
 
@@ -181,7 +251,7 @@ if(params.run_alignment) {
                     path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                     mode: "${params.publish_dir_mode}",
                     pattern: '*.bam',
-                    enabled: ( params.save_align_intermed || (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
+                    enabled: ( params.save_align_intermed || (!params.run_read_filter && !params.run_mark_dups && !params.run_remove_dups) )
                 ],
                 [
                     path: { "${params.outdir}/02_alignment/${params.aligner}/target/unmapped" },
@@ -221,7 +291,7 @@ if(params.run_alignment) {
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                 mode: "${params.publish_dir_mode}",
                 pattern: "*.{stats,flagstat,idxstats}",
-                enabled: ( params.save_align_intermed || (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
+                enabled: ( params.save_align_intermed || (!params.run_read_filter && !params.run_mark_dups && !params.run_remove_dups) )
             ]
         }
 
@@ -240,7 +310,7 @@ if(params.run_alignment) {
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                 mode: "${params.publish_dir_mode}",
                 pattern: "*.bam",
-                enabled: ( params.save_align_intermed || (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
+                enabled: ( params.save_align_intermed || (!params.run_read_filter && !params.run_mark_dups && !params.run_remove_dups) )
             ]
         }
 
@@ -260,7 +330,7 @@ if(params.run_alignment) {
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                 mode: "${params.publish_dir_mode}",
                 pattern: "*.bai",
-                enabled: ( params.save_align_intermed || (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
+                enabled: ( params.save_align_intermed || (!params.run_read_filter && !params.run_mark_dups && !params.run_remove_dups) )
             ]
         }
 
@@ -278,14 +348,14 @@ if(params.run_alignment) {
 
 /*
 ========================================================================================
-    Q-FILTERING
+    READ-FILTERING
 ========================================================================================
 */
 
-if(params.run_q_filter) {
+if(params.run_read_filter) {
     process {
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_VIEW_SORT_STATS:SAMTOOLS_VIEW' {
-            ext.args = "-b -q ${params.minimum_alignment_q_score}"
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_VIEW' {
+            ext.args = "-b -q ${params.minimum_alignment_q_score} -F 0x004 -F 0x0008 -f 0x001"
             ext.prefix = { "${meta.id}.target.filtered" }
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
@@ -295,7 +365,7 @@ if(params.run_q_filter) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_VIEW_SORT_STATS:SAMTOOLS_SORT' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_SORT' {
             ext.prefix = { "${meta.id}.target.filtered.sorted" }
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
@@ -305,7 +375,7 @@ if(params.run_q_filter) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_VIEW_SORT_STATS:SAMTOOLS_INDEX' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_INDEX' {
             ext.prefix = { "${meta.id}.target.filtered" }
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
@@ -315,7 +385,7 @@ if(params.run_q_filter) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_VIEW_SORT_STATS:BAM_STATS_SAMTOOLS:.*' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.target.filtered" }
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
@@ -327,6 +397,25 @@ if(params.run_q_filter) {
     }
 }
 
+/*
+========================================================================================
+    PRESEQ
+========================================================================================
+*/
+
+if (params.run_preseq) {
+    process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PRESEQ_LCEXTRAP' {
+            ext.args = "-v -B"
+            publishDir = [
+                path: { "${params.outdir}/04_reporting/preseq" },
+                mode: "${params.publish_dir_mode}",
+                pattern: "*.{log,txt}",
+            ]
+        }
+    }
+}
+
 /*
 ========================================================================================
     DUPLICATES
@@ -346,22 +435,17 @@ if(params.run_mark_dups) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:BAM_SORT_SAMTOOLS:.*' {
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                 mode: "${params.publish_dir_mode}",
-                pattern: "*.bai",
+                pattern: "*.{stats,flagstat,idxstats,bam,bai}",
                 enabled: ( params.save_align_intermed || (!params.run_remove_dups) )
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
-            publishDir = [
-                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
-                mode: "${params.publish_dir_mode}",
-                pattern: "*.{stats,flagstat,idxstats}",
-                enabled: ( params.save_align_intermed || (!params.run_remove_dups) )
-            ]
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
+            ext.prefix = { "${meta.id}.target.markdup.sorted" }
         }
     }
 }
@@ -379,22 +463,17 @@ if(params.run_remove_dups) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:SAMTOOLS_INDEX' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:BAM_SORT_SAMTOOLS:.*' {
             publishDir = [
                 path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
                 mode: "${params.publish_dir_mode}",
-                pattern: "*.bai",
+                pattern: "*.{stats,flagstat,idxstats,bam,bai}",
                 enabled: true
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:BAM_STATS_SAMTOOLS:.*' {
-            publishDir = [
-                path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
-                mode: "${params.publish_dir_mode}",
-                pattern: "*.{stats,flagstat,idxstats}",
-                enabled: true
-            ]
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
+            ext.prefix = { "${meta.id}.target.dedup.sorted" }
         }
     }
 }
@@ -407,15 +486,15 @@ if(params.run_remove_dups) {
 
 if (params.run_alignment) {
     process {
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_BT2_META:AWK_SCRIPT' {
-            ext.suffix = ".target"
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXTRACT_BT2_TARGET_META:AWK_SCRIPT' {
+            ext.suffix = "_meta_bt2_target"
             publishDir = [
                 enabled: false
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_BT2_SPIKEIN_META:AWK_SCRIPT' {
-            ext.suffix = ".dedup"
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXTRACT_BT2_SPIKEIN_META:AWK_SCRIPT' {
+            ext.suffix = "_meta_bt2_spikein"
             publishDir = [
                 enabled: false
             ]
@@ -425,8 +504,8 @@ if (params.run_alignment) {
 
 if (params.run_mark_dups) {
     process {
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:ANNOTATE_DEDUP_META:AWK' {
-            ext.suffix = ".awk"
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXTRACT_PICARD_DUP_META:AWK' {
+            ext.suffix = "_meta_picard_dups"
             ext.command = "'/^[^#]/{print}'"
             ext.command2 = " > int1.txt && head -2 int1.txt > int2.txt && sed 's/\\t/,/g' int2.txt > int3.txt && sed 's/.*/\\L&/g' int3.txt "
             publishDir = [
@@ -445,7 +524,7 @@ if (params.run_mark_dups) {
 if(params.run_peak_calling && (params.normalisation_mode == "Spikein" || params.normalisation_mode == "None")) {
     process {
         withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_GENOMECOV' {
-            ext.args = "-bg"
+            ext.args = params.extend_fragments ? '-bg -pc' : '-bg'
             publishDir = [
                 enabled: false
             ]
@@ -460,7 +539,8 @@ if(params.run_peak_calling && (params.normalisation_mode != "Spikein" && params.
                 '--outFileFormat bedgraph',
                 '--skipNAs',
                 "--binSize ${params.normalisation_binsize}",
-                "--normalizeUsing ${params.normalisation_mode}"
+                "--normalizeUsing ${params.normalisation_mode}",
+                params.extend_fragments ? '--extendReads' : '',
             ].join(' ').trim()
             ext.prefix = { "${meta.id}.bedgraph" }
             publishDir = [
@@ -506,10 +586,10 @@ if(params.run_peak_calling) {
 if(params.run_peak_calling && 'seacr' in params.callers) {
     process {
         withName: '.*:CUTANDRUN:SEACR_.*' {
-            ext.args   = "non stringent"
-            ext.prefix = { "${meta.id}.seacr.peaks.bed" }
+            ext.args   = "${params.seacr_norm} ${params.seacr_stringent}"
+            ext.prefix = { "${meta.id}.seacr.peaks" }
             publishDir = [
-                path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
+                path: { "${params.outdir}/03_peak_calling/04_called_peaks/seacr" },
                 mode: "${params.publish_dir_mode}",
                 pattern: "*.bed",
                 enabled: true
@@ -521,72 +601,29 @@ if(params.run_peak_calling && 'seacr' in params.callers) {
 if(params.run_peak_calling && 'macs2' in params.callers) {
     process {
         withName: '.*:CUTANDRUN:MACS2_.*' {
-            ext.args   = "-p ${params.macs2_pvalue}"
-            ext.prefix = { "${meta.id}.macs2.peaks.bed" }
-            publishDir = [
-                path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
-                mode: "${params.publish_dir_mode}",
-                pattern: "*.bed",
-                enabled: true
-            ]
-        }
-    }
-}
-
-/*
-========================================================================================
-    CONSENSUS PEAKS
-========================================================================================
-*/
-
-if(params.run_peak_calling) {
-    process {
-        withName: '.*:AWK_NAME_PEAK_BED' {
-            ext.command = "'{OFS = \"\\t\"} {print \$0, FILENAME}'"
-            ext.ext     = "bed"
-            publishDir = [
-                enabled: false
-            ]
-        }
-
-        withName: '.*:CONSENSUS_PEAKS:SORT|.*:CONSENSUS_PEAKS_ALL:SORT' {
-            ext.args   = "-k1,1 -k2,2n"
-            ext.ext    = "bed"
-            publishDir = [
-                enabled: false
-            ]
-        }
-
-        withName: '.*:CONSENSUS_PEAKS:BEDTOOLS_MERGE|.*:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
-            ext.args   = " -c 2,3,4,5,6,7,7 -o collapse,collapse,collapse,collapse,collapse,collapse,count_distinct"
-            ext.prefix = { "${meta.id}.consensus.peaks" }
+            ext.args   = [
+                "-p ${params.macs2_pvalue}",
+                params.macs2_narrow_peak ? '' : "--broad --broad-cutoff ${params.macs2_broad_cutoff}"
+            ].join(' ').trim()
+            ext.prefix = { "${meta.id}.macs2" }
             publishDir = [
-                path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
+                path: { "${params.outdir}/03_peak_calling/04_called_peaks/macs2" },
                 mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                pattern: "*.{bed,narrowPeak,broadPeak,xls}",
                 enabled: true
             ]
         }
-
-        withName: '.*:CONSENSUS_PEAKS:PLOT_CONSENSUS_PEAKS|.*:CONSENSUS_PEAKS_ALL:PLOT_CONSENSUS_PEAKS' {
-            publishDir = [
-                path: { "${params.outdir}/04_reporting" },
-                mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: params.skip_upset_plots
-            ]
-        }
     }
 }
 
-if(params.run_peak_calling && !params.run_consensus_all) {
+if(params.run_peak_calling && 'macs2' in params.callers) {
     process {
-        withName: '.*:CONSENSUS_PEAKS:AWK' {
-            ext.command = "' \$10 >= " + params.replicate_threshold.toString() + " {print \$0}'"
+        withName: '.*:CUTANDRUN:PEAK_TO_BED' {
+            ext.args    = "-f 1-6"
             ext.ext     = "bed"
-            ext.suffix  = ".consensus.peaks.filtered"
+            ext.suffix  = ".macs2.peaks"
             publishDir  = [
-                path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
+                path: { "${params.outdir}/03_peak_calling/04_called_peaks/macs2" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -595,16 +632,13 @@ if(params.run_peak_calling && !params.run_consensus_all) {
     }
 }
 
-if(params.run_peak_calling && params.run_consensus_all) {
+if(params.run_peak_calling && params.callers[0] == 'seacr') {
     process {
-        withName: '.*:CONSENSUS_PEAKS_ALL:AWK' {
-            ext.command = "' \$10 >= " + params.replicate_threshold.toString() + " {print \$0}'"
-            ext.ext    = "bed"
-            publishDir = [
-                path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
-                mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: true
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:AWK_EXTRACT_SUMMITS' {
+            ext.command = "'{split(\$6, summit, \":\"); split(summit[2], region, \"-\"); print summit[1]\"\\t\"region[1]\"\\t\"region[2]}'"
+            ext.suffix  = ".max_signal"
+            publishDir  = [
+                enabled: false
             ]
         }
     }
@@ -612,77 +646,45 @@ if(params.run_peak_calling && params.run_consensus_all) {
 
 /*
 ========================================================================================
-    CALCULATE FRAGMENTS
+    CONSENSUS PEAKS
 ========================================================================================
 */
 
 if(params.run_peak_calling) {
     process {
-        withName: '.*:CALCULATE_FRAGMENTS:SAMTOOLS_VIEW' {
-            ext.args = "-F 0x04 -b"
-            ext.prefix = { "${meta.id}.mapped" }
-            publishDir = [
-                enabled: false
-            ]
-        }
-
-        withName: '.*:CALCULATE_FRAGMENTS:SAMTOOLS_SORT' {
-            ext.args = "-n"
-            ext.prefix = { "${meta.id}.mapped.sorted" }
-            publishDir = [
-                enabled: false
-            ]
-        }
-
-        withName: '.*:CALCULATE_FRAGMENTS:BEDTOOLS_BAMTOBED' {
-            ext.args = "-bedpe"
+        withName: '.*:AWK_NAME_PEAK_BED' {
+            ext.command = "'{OFS = \"\\t\"} {print \$0, FILENAME}'"
+            ext.ext     = "bed"
             publishDir = [
                 enabled: false
             ]
         }
 
-        withName: '.*:CALCULATE_FRAGMENTS:AWK' {
-            ext.command = "'\$1==\$4 && \$6-\$2 < 1000 {print \$0}'"
-            ext.suffix = ".filt"
+        withName: '.*:CONSENSUS_PEAKS:SORT|.*:CONSENSUS_PEAKS_ALL:SORT' {
+            ext.args   = "-k1,1 -k2,2n"
             ext.ext    = "bed"
             publishDir = [
                 enabled: false
             ]
         }
 
-        withName: '.*:CALCULATE_FRAGMENTS:CUT' {
-            ext.args    = "-f 1,2,6"
-            ext.command = "| sort -T '.' -k1,1 -k2,2n -k3,3n"
-            ext.suffix  = ".frags"
-            ext.ext     = "bed"
-            publishDir  = [
-                path: { "${params.outdir}/03_peak_calling/06_fragments" },
-                mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: true
-            ]
-        }
-
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:AWK_FRAG_BIN' {
-            ext.args     = "-v w=500"
-            ext.command  = "'{print \$1, int((\$2 + \$3)/(2*w))*w + w/2, FILENAME}'"
-            ext.command2 = "| sort -T '.' -k1,1V -k2,2n | uniq -c | awk -v OFS=\"\\t\" '{print \$2, \$3, \$1, \$4}' | sort -T '.' -k1,1V -k2,2n"
-            ext.suffix   = ".frags.bin500"
-            ext.ext      = "bed"
-            publishDir   = [
-                path: { "${params.outdir}/03_peak_calling/06_fragments" },
+        withName: '.*:CONSENSUS_PEAKS:BEDTOOLS_MERGE|.*:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
+            ext.args   = " -c 2,3,4,5,6,7,7 -o collapse,collapse,collapse,collapse,collapse,collapse,count_distinct"
+            ext.prefix = { "${meta.id}.consensus.peak_counts" }
+            publishDir = [
+                path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_CUSTOMVIEW' {
-            ext.args     = "-F 0x04"
-            ext.args2    = "awk -F'\\t' 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs(\$9)}' | sort -T '.' | uniq -c | awk -v OFS=\"\\t\" '{print \$2, \$1/2}'"
-            ext.suffix   = ".frags.len"
-            publishDir   = [
-                path: { "${params.outdir}/03_peak_calling/06_fragments" },
+        withName: '.*:CONSENSUS_PEAKS:AWK|.*:CONSENSUS_PEAKS_ALL:AWK' {
+            ext.command = "' \$10 >= " + params.replicate_threshold.toString() + " {print \$0}'"
+            ext.ext     = "bed"
+            ext.suffix  = ".consensus.peaks"
+            publishDir  = [
+                path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -710,20 +712,12 @@ if(params.run_reporting && params.run_igv) {
     }
 }
 
-if(params.run_reporting && params.run_deep_tools) {
+if(params.run_reporting && params.run_deeptools_heatmaps) {
     process {
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:AWK_EDIT_PEAK_BED' {
-            ext.command = "'{split(\$6, summit, \":\"); split(summit[2], region, \"-\"); print summit[1]\"\\t\"region[1]\"\\t\"region[2]}'"
-            ext.suffix  = ".max_signal"
-            publishDir  = [
-                enabled: false
-            ]
-        }
-
         withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {
-            ext.args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros --missingDataAsZero"
+            ext.args = "scale-regions --beforeRegionStartLength ${params.dt_heatmap_gene_beforelen} --regionBodyLength ${params.dt_heatmap_gene_bodylen} --afterRegionStartLength ${params.dt_heatmap_gene_afterlen} --skipZeros --missingDataAsZero"
             publishDir   = [
-                path: { "${params.outdir}/04_reporting/heatmaps/gene" },
+                path: { "${params.outdir}/04_reporting/deeptools_heatmaps/gene" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -733,7 +727,7 @@ if(params.run_reporting && params.run_deep_tools) {
         withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_GENE' {
             ext.args = "--sortUsing sum"
             publishDir   = [
-                path: { "${params.outdir}/04_reporting/heatmaps/gene" },
+                path: { "${params.outdir}/04_reporting/deeptools_heatmaps/gene" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -741,9 +735,9 @@ if(params.run_reporting && params.run_deep_tools) {
         }
 
         withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {
-            ext.args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros --missingDataAsZero"
+            ext.args = "reference-point -a ${params.dt_heatmap_peak_beforelen} -b ${params.dt_heatmap_peak_afterlen} --referencePoint center --skipZeros --missingDataAsZero"
             publishDir   = [
-                path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
+                path: { "${params.outdir}/04_reporting/deeptools_heatmaps/peaks" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -753,7 +747,7 @@ if(params.run_reporting && params.run_deep_tools) {
         withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {
             ext.args = "--sortUsing sum --startLabel \"Peak Start\" --endLabel \"Peak End\" --xAxisLabel \"\" --regionsLabel \"Peaks\""
             publishDir   = [
-                path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
+                path: { "${params.outdir}/04_reporting/deeptools_heatmaps/peaks" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
@@ -762,15 +756,108 @@ if(params.run_reporting && params.run_deep_tools) {
     }
 }
 
-if(params.run_reporting) {
+if(params.run_reporting && params.run_deeptools_qc) {
     process {
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CALCULATE_FRIP' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY' {
+                ext.args = "--smartLabels --binSize ${params.dt_qc_bam_binsize}"
+                publishDir   = [
+                    path: { "${params.outdir}/04_reporting/deeptools_qc" },
+                    mode: "${params.publish_dir_mode}",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                    enabled: true
+                ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_PLOTCORRELATION' {
+                ext.args = "--corMethod spearman --whatToPlot heatmap --skipZeros"
+                publishDir   = [
+                    path: { "${params.outdir}/04_reporting/deeptools_qc" },
+                    mode: "${params.publish_dir_mode}",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                    enabled: true
+                ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_PLOTPCA' {
+                ext.args = ""
+                publishDir   = [
+                    path: { "${params.outdir}/04_reporting/deeptools_qc" },
+                    mode: "${params.publish_dir_mode}",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                    enabled: true
+                ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_PLOTFINGERPRINT' {
+                ext.args = "--skipZeros"
+                publishDir   = [
+                    path: { "${params.outdir}/04_reporting/deeptools_qc" },
+                    mode: "${params.publish_dir_mode}",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                    enabled: true
+                ]
+        }
+    }
+}
+
+if (params.run_reporting && params.run_peak_qc) {
+    process {
+        withName: '.*:EXTRACT_FRAGMENTS:SAMTOOLS_SORT' {
+            ext.args = "-n"
+            ext.prefix = { "${meta.id}.sortedbyname" }
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:EXTRACT_FRAGMENTS:BEDTOOLS_BAMTOBED' {
+            ext.args = "-bedpe"
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:EXTRACT_FRAGMENTS:AWK' {
+            ext.command = "'\$1==\$4 && \$6-\$2 < 1000 {print \$0}'"
+            ext.suffix = ".filt"
+            ext.ext    = "bed"
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: '.*:EXTRACT_FRAGMENTS:CUT' {
+            ext.args    = "-f 1,2,6"
+            ext.command = "| sort -T '.' -k1,1 -k2,2n -k3,3n"
+            ext.suffix  = ".frags"
+            ext.ext     = "bed"
             publishDir  = [
+                path: { "${params.outdir}/03_peak_calling/06_fragments_from_bams" },
+                mode: "${params.publish_dir_mode}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: true
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PEAK_FRIP' {
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PRIMARY_PEAK_COUNTS' {
+            publishDir = [
                 enabled: false
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CUT_CALC_REPROD' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:CONSENSUS_PEAK_COUNTS' {
+            publishDir = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:CUT_CALC_REPROD' {
             ext.args   = "-f 1,2,3,6"
             ext.suffix = ".repro"
             ext.ext    = "bed"
@@ -779,48 +866,49 @@ if(params.run_reporting) {
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_INTERSECT' {
-            ext.args   = "-C -sorted"
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:BEDTOOLS_INTERSECT' {
+            ext.args   = "-C -sorted -f ${params.min_peak_overlap}"
             publishDir  = [
                 enabled: false
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CALCULATE_PEAK_REPROD' {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:CALCULATE_PEAK_REPROD' {
             publishDir  = [
                 enabled: false
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META' {
-            publishDir   = [
-                path: { "${params.outdir}/04_reporting" },
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS' {
+            publishDir = [
+                path: { "${params.outdir}/04_reporting/consensus_upset_plots" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
             ]
         }
+    }
+}
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META_CTRL' {
+if(params.run_reporting) {
+    process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_CUSTOMVIEW' {
+            ext.args     = "-F 0x04"
+            ext.args2    = "awk -F'\\t' 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs(\$9)}' | sort -T '.' | uniq -c | awk -v OFS=\"\\t\" '{print \$2, \$1/2}'"
+            ext.suffix   = ".frags.len"
             publishDir   = [
-                path: { "${params.outdir}/04_reporting" },
+                path: { "${params.outdir}/03_peak_calling/06_fragments_from_bams" },
                 mode: "${params.publish_dir_mode}",
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: true
             ]
         }
 
-        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:GENERATE_REPORTS' {
-            publishDir   = [
-                path: { "${params.outdir}/04_reporting/qc" },
-                mode: "${params.publish_dir_mode}",
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: true
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FRAG_LEN_HIST' {
+            publishDir  = [
+                enabled: false
             ]
         }
-
-
-
     }
 }
 
@@ -836,3 +924,4 @@ if (params.run_multiqc) {
         }
     }
 }
+
diff --git a/conf/resources.config b/conf/resources.config
index da18803b..d6cb5942 100644
--- a/conf/resources.config
+++ b/conf/resources.config
@@ -2,37 +2,27 @@
 ========================================================================================
     nf-core/cutandrun Nextflow resource config file
 ========================================================================================
-    Minimal and process-specific resource allocation.
+    Process-specific resource allocation.
 ----------------------------------------------------------------------------------------
 */
 
 /*
 ========================================================================================
-    MINIMAL AND ULTRA LOW RESOURCE ALLOCATION
+    MODULE-SPECIFIC RESOURCE ALLOCATION
 ========================================================================================
 */
 
-process {
-    withLabel:process_min {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withLabel:process_ultralow {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+if(params.run_genome_prep) {
+    process {
+        withName: '.*:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT' {
+            cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 1.h   * task.attempt, 'time'    ) }
+        }
     }
 }
 
-/*
-========================================================================================
-    MODULE-SPECIFIC RESOURCE ALLOCATION
-========================================================================================
-*/
-
-process {
+if(params.run_alignment) {
     withName: '.*:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {
         cpus   = { check_max( 32     * task.attempt, 'cpus'    ) }
         memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
@@ -44,127 +34,42 @@ process {
         memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h    * task.attempt, 'time'    ) }
     }
+}
 
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {
-        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h    * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {
-        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h    * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_INDEX' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_IDXSTATS' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_FLAGSTAT' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: '.*CHROMSIZES' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
-    }
-
-    // 1 CPU 8 GB
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_GENOMECOV' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_SORT' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_INTERSECT' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: '.*:CONSENSUS_PEAKS:BEDTOOLS_MERGE|.*:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDCLIP' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    // ultralow
-    withName: '.*:CALCULATE_FRAGMENTS:BEDTOOLS_BAMTOBED' {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SEACR_CALLPEAK' {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC' {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
-    }
-
-    // memory
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+if(params.run_reporting) {
+    process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FRAG_LEN_HIST' {
+            cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 4.h    * task.attempt, 'time'    ) }
+        }
     }
+}
 
-    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_VIEW' {
-        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+if(params.run_reporting && params.run_deeptools_heatmaps) {
+    process {
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {
+            cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 4.h    * task.attempt, 'time'    ) }
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {
+            cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 4.h    * task.attempt, 'time'    ) }
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_GENE' {
+            cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        }
+
+        withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {
+            cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+            memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }
+            time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        }
     }
 }
diff --git a/conf/test.config b/conf/test.config
index afecb63f..1cc9016b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -30,6 +30,4 @@ params {
     blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
     spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_fasta_only.config b/conf/test_fasta_only.config
index e420f97d..8916f4cf 100644
--- a/conf/test_fasta_only.config
+++ b/conf/test_fasta_only.config
@@ -15,6 +15,4 @@ params {
     bowtie2            = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz'
     spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index d52dec47..e47972b4 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,7 +15,6 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     genome = 'GRCh38'
+    gene_bed = null
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all.csv'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full_multi.config b/conf/test_full_multi.config
index b7da5111..76e866d7 100644
--- a/conf/test_full_multi.config
+++ b/conf/test_full_multi.config
@@ -16,6 +16,4 @@ params {
 
     genome = 'GRCh38'
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep.csv'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full_small.config b/conf/test_full_small.config
index e05bbe85..ea86419f 100644
--- a/conf/test_full_small.config
+++ b/conf/test_full_small.config
@@ -18,6 +18,4 @@ params {
     blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
     spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full_small_local_zip.config b/conf/test_full_small_local_zip.config
index 89812236..747087ad 100644
--- a/conf/test_full_small_local_zip.config
+++ b/conf/test_full_small_local_zip.config
@@ -18,6 +18,4 @@ params {
     blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
     spikein_fasta      = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_local_zip.config b/conf/test_local_zip.config
index 84b09fe2..71a71c82 100644
--- a/conf/test_local_zip.config
+++ b/conf/test_local_zip.config
@@ -30,6 +30,4 @@ params {
     blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
     spikein_fasta      = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/conf/test_no_control.config b/conf/test_no_control.config
index fa4a6c98..df051a7b 100644
--- a/conf/test_no_control.config
+++ b/conf/test_no_control.config
@@ -31,6 +31,5 @@ params {
     spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
 
-    minimum_alignment_q_score = 10
     use_control               = false
 }
diff --git a/conf/test_tech_reps.config b/conf/test_tech_reps.config
index ead5004c..00c7526a 100644
--- a/conf/test_tech_reps.config
+++ b/conf/test_tech_reps.config
@@ -30,6 +30,4 @@ params {
     blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
     spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
     spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
-
-    minimum_alignment_q_score = 10
 }
diff --git a/docs/images/consensus_peaks.png b/docs/images/consensus_peaks.png
deleted file mode 100644
index 9e5c0a49..00000000
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deleted file mode 100755
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similarity index 100%
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rename to docs/images/output/all_consensus_peaks.png
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diff --git a/docs/images/py_frags_in_peaks.png b/docs/images/py_frags_in_peaks.png
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diff --git a/docs/output.md b/docs/output.md
index f358d36c..c37a4fbe 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,50 +1,64 @@
-# nf-core/cutandrun: Output
+<!-- vscode-markdown-toc -->
+
+- 1. [Introduction](#Introduction)
+- 2. [Preprocessing](#Preprocessing)
+     - 2.1. [Sample Sheet Check](#SampleSheetCheck)
+     - 2.2. [FASTQ Merging](#FASTQMerging)
+     - 2.3. [FastQC](#FastQC)
+     - 2.4. [Sequence Counts](#SequenceCounts)
+       - 2.4.1. [Sequence Quality](#SequenceQuality)
+       - 2.4.2. [Overrepresented Sequences](#OverrepresentedSequences)
+     - 2.5. [TrimGalore](#TrimGalore)
+- 3. [Alignment](#Alignment)
+     - 3.1. [Bowtie 2](#Bowtie2)
+     - 3.2. [Library Complexity](#LibraryComplexity)
+- 4. [Alignment post-processing](#Alignmentpost-processing)
+     - 4.1. [Quality Filtering](#QualityFiltering)
+     - 4.2. [PICARD MarkDuplicates/RemoveDuplicates](#PICARDMarkDuplicatesRemoveDuplicates)
+- 5. [Fragment-based QC](#Fragment-basedQC)
+     - 5.1. [PCA](#PCA)
+     - 5.2. [Fingerprint](#Fingerprint)
+     - 5.3. [Correlation](#Correlation)
+- 6. [Peak Calling](#PeakCalling)
+     - 6.1. [Bam to bedgraph](#Bamtobedgraph)
+     - 6.2. [Bed to bigwig](#Bedtobigwig)
+     - 6.3. [SEACR peak calling](#SEACRpeakcalling)
+     - 6.4. [MACS2 peak calling](#MACS2peakcalling)
+     - 6.5. [Consensus Peaks](#ConsensusPeaks)
+- 7. [Peak-based QC](#Peak-basedQC)
+     - 7.1. [Peak Counts](#PeakCounts)
+     - 7.2. [Peak Reproducibility](#PeakReproducibility)
+     - 7.3. [FRiP Score](#FRiPScore)
+- 8. [Fragment Length Distribution](#FragmentLengthDistribution)
+     - 8.1. [Heatmaps](#Heatmaps)
+     - 8.2. [Upset Plots](#UpsetPlots)
+     - 8.3. [IGV](#IGV)
+- 9. [Workflow reporting and genomes](#Workflowreportingandgenomes)
+     - 9.1. [Reference genome files](#Referencegenomefiles)
+     - 9.2. [Pipeline information](#Pipelineinformation)
+
+<!-- vscode-markdown-toc-config
+    numbering=true
+    autoSave=true
+    /vscode-markdown-toc-config -->
+
+<!-- /vscode-markdown-toc -->
+
+## 1. <a name='Introduction'></a>Introduction
+
+This document describes the output produced by the pipeline. This document can be used as a general guide for CUT&RUN analysis. Unless specified all outputs shown are from the MultiQC report generated at the end of the pipeline run.
 
-## Introduction
+The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-This document describes the output produced by the pipeline. Example plots are taken from the pdf report which details summary details and analyses specific to CUT&Run/CUT&Tag data, and the MultiQC report, which summarises results from some tools used, at the end of the pipeline.
+## 2. <a name='Preprocessing'></a>Preprocessing
 
-The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
+### 2.1. <a name='SampleSheetCheck'></a>Sample Sheet Check
+
+The first step of the pipeline is to verify the sample sheet structure and experimental design to ensure that it is valid.
 
-## Pipeline overview
-
-The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
-
-- [nf-core/cutandrun: Output](#nf-corecutandrun-output)
-  - [Introduction](#introduction)
-  - [Pipeline overview](#pipeline-overview)
-  - [Preprocessing](#preprocessing)
-    - [Samplesheet check](#samplesheet-check)
-    - [Fastq merging](#fastq-merging)
-    - [FastQC](#fastqc)
-    - [TrimGalore](#trimgalore)
-  - [Alignment](#alignment)
-    - [Bowtie 2](#bowtie-2)
-  - [Alignment post-processing](#alignment-post-processing)
-    - [samtools](#samtools)
-    - [picard MarkDuplicates/RemoveDuplicates](#picard-markduplicatesremoveduplicates)
-  - [Peak Calling](#peak-calling)
-    - [Bam to bedgraph](#bam-to-bedgraph)
-    - [Clip bedfiles](#clip-bedfiles)
-    - [Bed to bigwig](#bed-to-bigwig)
-    - [SEACR peak calling](#seacr-peak-calling)
-    - [BEDtools](#bedtools)
-  - [Reporting](#reporting)
-    - [Python reporting](#python-reporting)
-    - [MultiQC](#multiqc)
-    - [IGV](#igv)
-    - [Deeptools](#deeptools)
-  - [Workflow reporting and genomes](#workflow-reporting-and-genomes)
-    - [Reference genome files](#reference-genome-files)
-    - [Pipeline information](#pipeline-information)
-
-## Preprocessing
-
-### Samplesheet check
-
-The first step of the pipeline is to verify the samplesheet structure and experimental design to ensure that it is valid.
-
-### Fastq merging
+### 2.2. <a name='FASTQMerging'></a>FASTQ Merging
+
+If multiple libraries/runs have been provided for the same sample in the input sample sheet (e.g. to increase sequencing depth), then these will be merged at the very beginning of the pipeline. Please refer to the [usage documentation](https://nf-co.re/rnaseq/usage#samplesheet-input) to see how to specify this type of sample in the input sample sheet.
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -54,9 +68,7 @@ The first step of the pipeline is to verify the samplesheet structure and experi
 
 </details>
 
-If multiple libraries/runs have been provided for the same sample in the input samplesheet (e.g. to increase sequencing depth) then these will be merged at the very beginning of the pipeline in order to have consistent sample naming throughout the pipeline. Please refer to the [usage documentation](https://nf-co.re/rnaseq/usage#samplesheet-input) to see how to specify these samples in the input samplesheet.
-
-### FastQC
+### 2.3. <a name='FastQC'></a>FastQC
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -71,11 +83,77 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
+We perform FastQC on reads before and after trimming. The descriptions below apply to both reporting unless explicitly mentioned.
+
+### 2.4. <a name='SequenceCounts'></a>Sequence Counts
+
+This first FastQC report provides a first look at how many reads your FASTQ files contain. Predicted duplicates are also shown in black however, we recommend using the PICARD duplicate reports as they are more detailed and accurate.
+
+As a general rule of thumb for an abundant epitope like H3K27me3, we recommend no fewer than 5M aligned reads, the sequence counts must reflect this number plus any unaligned error reads. Assuming a max alignment error rate of 20%, we recommend a minimum read count of 6M raw reads. Less abundant epitopes may require deeper sequencing for a good signal.
+
+Another thing to look out for in this plot is the consistency of reads across your various groups and replicates. Large differences in the number of reads between biological replicates may be indicative of technical variation arising due to human error, or problems with the wet-lab protocol or sequencing process.
+
+![MultiQC - FastQC sequence counts plot](images/output/mqc_01_fastqc_sequence_counts.png)
+
+#### 2.4.1. <a name='SequenceQuality'></a>Sequence Quality
+
+FastQC provides several reports that look at sequence quality from different views. The mean quality scores plot shows the sequence quality along the length of the read. It is normal to see some drop off in quality towards the end of the read, especially with long-read sequencing (150 b.p.). The plot should be green and with modern sequencing on good quality samples, should be > 30 throughout the majority of the read. There are many factors that affect the read quality but users can expect drops in average score when working with primary tissue or other tissues that are difficult to sequence.
+
+![mqc_02_fastqc_per_base_sequence_quality](images/output/mqc_02_fastqc_per_base_sequence_quality.png)
+
+The Per-sequence quality score report shows a different view of sequencing quality, showing the distribution of scores for each sample. This chart will peak where the majority of the reads are scored. In modern Illumina sequencing this should be curve at the end of the chart in an area > 30.
+
+![f](images/output/mqc_03_fastqc_per_sequence_quality_scores.png)
+
+The Per-base sequence quality report is not applicable to CUT&RUN data generally. Any discordant sequence content at the beginning of the reads is a common phenomenon for CUT&RUN reads. Failing to pass the Per-base sequence content does not mean your data failed. It can be due to Tn5 preferential binding or what you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling.
+
+The Per-sequence GC content report shows the distribution of the GC content of all reads in a sample. This should be centred around the average GC content % for your target organism.
+
+![mqc_04_fastqc_per_sequence_gc_content](images/output/mqc_04_fastqc_per_sequence_gc_content.png)
+
+An unusually shaped distribution such as one with dual peaks could indicate a contaminated library or some other kind of biased subset. In the image below, we see a signifiant batch effect between two groups of samples run on different days. The samples in red most likely are contaminated with DNA that has a different GC content to that of the target organism.
+
+![plot](images/output/mqc_05_fastqc_per_sequence_gc_content.png)
+
+#### 2.4.2. <a name='OverrepresentedSequences'></a>Overrepresented Sequences
+
+FastQC provides three reports that focus on overrepresented sequences at the read level. All three must be looked at both before and after trimming to gain a detailed view of the types of sequence duplication that your samples contain.
+
+A normal high-throughput library will contain a diverse set of sequences with no individual sequence making up a large fraction of the whole library. Finding that a single sequence is overrepresented can be biologically significant, however it also often indicates that the library is contaminated, or is not as diverse as expected.
+
+The sequence duplication level plot shows percentages of the library that has a particular range of duplication counts. For example, the plot below shows that for some samples ~10% of the library has > 100 duplicated sequences. While not particularly informative on its own, if problems are identified in subsequent reports, it can help to identify the scale of the duplication problem.
 
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
+![plot](images/output/mqc_06_fastqc_sequence_duplication_levels.png)
 
-### TrimGalore
+The second two reports must be analysed together both before and after trimming for maximum insight. The first report, overrepresented sequences, shows the percentage of identified sequences in each library; the second, adapter content, shows a cumulative plot of adapter content at each base position. Due to the short insert length for CUT&RUN, short read length sequencing (25 b.p.) is possible for samples; consequently, when the sequencing length increases, more of the sequencing adapters will be sequenced. Adapter sequences should always be trimmed off, therefore, it is important to look at both of these plots after trimming as well to check that the adapter content has been removed and there are only small levels of overrepresented sequences. A clear adapter content plot after trimming but where there are still significant levels of overrepresented sequences could indicate something biologically significant or experimental error such as contamination.
+
+**A 25 b.p CUT&Tag experiment with clear reports even before trimming**
+
+![plot](images/output/mqc_07_fastqc_clear_overrep.png)
+
+**A 150 b.p. CUT&RUN experiment with significant adapter content before trimming but that is clear after trimming**
+
+![plot](images/output/mqc_08_fastqc_adapter_content.png)
+
+![plot](images/output/mqc_10_fastqc_overrepresented_sequences.png)
+
+**After trimming**
+
+![plot](images/output/mqc_07_fastqc_clear_overrep.png)
+
+**CUT&RUN experiment that shows over represented sequences even after trimming all the adapter content away**
+
+![plot](images/output/mqc_11_fastqc_overrepresented_sequences.png)
+
+![plot](images/output/mqc_12_fastqc_adapter_content.png)
+
+**After trimming**
+
+![plot](images/output/mqc_13_fastqc_overrepresented_sequences.png)
+
+![plot](images/output/mqc_09_fastqc_clear_adapter.png)
+
+### 2.5. <a name='TrimGalore'></a>TrimGalore
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -93,11 +171,13 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 > **NB:** TrimGalore! will only run using multiple cores if you are able to use more than > 5 and > 6 CPUs for single- and paired-end data, respectively. The total cores available to TrimGalore! will also be capped at 4 (7 and 8 CPUs in total for single- and paired-end data, respectively) because there is no longer a run-time benefit. See [release notes](https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019) and [discussion whilst adding this logic to the nf-core/atacseq pipeline](https://github.com/nf-core/atacseq/pull/65).
 
-![MultiQC - cutadapt trimmed sequence length plot](images/mqc_cutadapt_trimmed.png)
+**Typical plot showing many small sequences being trimmed from reads**
+
+![MultiQC - cutadapt trimmed sequence length plot](images/output/mqc_14_fastqc_cutadapt_trimmed.png)
 
-## Alignment
+## 3. <a name='Alignment'></a>Alignment
 
-### Bowtie 2
+### 3.1. <a name='Bowtie2'></a>Bowtie 2
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -106,34 +186,51 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 </details>
 
-Adapter-trimmed reads are mapped to the target and spike-in genomes using [Bowtie 2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). A genome index is required to run Bowtie2 which is created automatically from the genome fasta input.
-
-The pipeline will output the `.bam` files with index and samtools stats for only the final set by default. For example, the full pipeline will only output picard duplicates processed files as this is the final step before peak calling. If the pipeline is run with `--only_align`, then the `bam` files from the initial sorting and indexing will be copied to the output directory as the other steps are not run.
+Adapter-trimmed reads are mapped to the target and spike-in genomes using [Bowtie 2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). The pipeline will output the `.bam` files with index and samtools stats for only the final set by default. For example, the full pipeline will only output picard duplicates processed files as this is the final step before peak calling. If the pipeline is run with `--only_align`, then the `bam` files from the initial sorting and indexing will be copied to the output directory as the other steps are not run.
 
 If `--save_align_intermed` is specified then all the `bam` files from all stages will be copied over to the output directory.
 
 If `--save_spikein_aligned` is specified then the spike-in alignment files will also be published.
 
-![MultiQC - Bowtie2 paired-end mapping stats](images/mqc_bowtie2_pe.png)
+MultiQC shows several alignment-based reports however, the most important is the alignment score plot. A typical plot for a well-defined genome will look like the image below with high alignment scores and low levels of multi-mapped and unaligned sequences. Low levels of alignment can be due to a multitude of different factors but is generally a strong sign that the input library was of poor quality. That being said, if the total number of aligned reads is still above the required level for the target epitope abundance then it does not mean the sample has failed, as there still may be enough information to answer the biological question asked.
 
-## Alignment post-processing
+![MultiQC - Bowtie2 paired-end mapping stats](images/output/mqc_15_bowtie2_pe.png)
 
-### samtools
+The MultiQC report also includes a spike-in alignment report. This plot is important for deciding whether to normalise your samples using the spike-in genome or by another method. The default mode in the pipeline is to normalise stacked reads before peak calling for epitope abundance using spike-in normalisation.
 
-<details markdown="1">
-<summary>Output files</summary>
+Traditionally, E. coli DNA is carried along with bacterially-produced enzymes that are used in CUT&RUN and CUT&Tag experiments and gets tagmented non-specifically during the reaction. The fraction of total reads that map to the E.coli genome depends on the yield of the epitope targeted, and so depends on the number of cells used and the abundance of that epitope in chromatin. Since a constant amount of protein is added to the reactions and brings along a fixed amount of E. coli DNA, E. coli reads can be used to normalise against epitope abundance in a set of experiments. This is assuming that the amount of E.coli and the numbers of cells is consistent between samples.
+
+Since the introduction of these techniques there are several factors that have reduced the usefulness of this type of normalisation in certain experimental conditions. Firstly, many commercially available kits now have very low levels of E.coli DNA in them, which therefore requires users to spike-in their own DNA for normalisation which is not always done. Secondly the normalisation approach is dependant on the cell count between samples being constant, which in our experience is quite difficult to achieve especially in primary tissue samples.
+
+The image below shows a typical plot for samples that have the correct amount of spike-in DNA for normalisation. The target samples have usually < 1% spike-in alignment (but still with > 1000 reads to reach above noise thresholds) while IgG should have the most as it has a large abundance (2-5%). In this example, the IgG will be brought inline with the other epitopes enabling proper peak calling using the IgG as a background.
+
+![plot](images/output/mqc_16_spikein_bowtie2_pe_plot.png)
+
+If you see very low spike-in levels for all samples, it is likely your Tn5 had no residual E.coli DNA and that no additional spike-in DNA was added. In this case spike-in normalisation cannot be used and normalisation must be switched to read count or no normalisation at all.
+
+If you see a strange distribution of spike-in DNA alignment that does not fit with your knowledge of the relative abundance of your IgG and target epitopes, this is indicative of a problem with the spike-in process and again, another normalisation option should be chosen.
 
-- `aligner/bowtie2/intermediate/`
-  - `.filtered.bam`: If `--publish_align_intermeds` is specified the original BAM file containing read alignments to the target genome will be placed in this directory.
-  - `.filtered.bam.bai`: BAI file for BAM.
-- `aligner/bowtie2/intermediate/samtools_stats`
-  - `.filtered.bam.*stats`: various statistics regarding the BAM files.
+In the plot below, it may initially look as though the spike-in distribution is too varied to be useful however, the larger IgG spike-in alignment counts correspond to the target samples with more sequencing depth and more spike-in alignments; therefore, these samples are actually good candidates for spike-in normalisation.
+
+![plot](images/output/mqc_17_bowtie2_pe_plot.png)
+
+### 3.2. <a name='LibraryComplexity'></a>Library Complexity
+
+To estimate library complexity and identify potentially over-sequenced libraries (or libraries with a low information content) we run preseq. [Library Complexity](http://smithlabresearch.org/software/preseq/) estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.
+
+The plot below shows a group of samples where the majority of unique molecules are accounted for by 50M. The total molecules detected stretches beyond 250M indicating the library is over sequenced and that an identical future experiment could be sequenced to a lower depth without loosing information.
+
+![plot](images/output/mqc_18_preseq_plot.png)
+
+## 4. <a name='Alignmentpost-processing'></a>Alignment post-processing
+
+### 4.1. <a name='QualityFiltering'></a>Quality Filtering
 
 </details>
 
-BAM files are filtered for a minimum quality score of 0 using [SAMtools](http://samtools.sourceforge.net/).
+BAM files are filtered for a minimum quality score and for fully mapped reads using [SAMtools](http://samtools.sourceforge.net/). These results are then passed on to Picard for duplicate removal.
 
-### picard MarkDuplicates/RemoveDuplicates
+### 4.2. <a name='PICARDMarkDuplicatesRemoveDuplicates'></a>PICARD MarkDuplicates/RemoveDuplicates
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -150,11 +247,45 @@ By default, the pipeline uses [picard MarkDuplicates](https://broadinstitute.git
 
 If your data includes IgG controls, these will additionally be de-duplicated. It is not the normal protocol to de-duplicate the target reads, however, if this is required, use the `--dedup_target_reads true` switch.
 
-![MultiQC - Picard MarkDuplicates metrics plot](images/mqc_picard_markduplicates.png)
+The plot below shows a typical CUT&Tag experiment that has its PCR cycles optimised. We see a low level of non-optical duplication (from library amplification) in the target samples but more in the IgG samples as the reads in these samples derive from non-specific tagmentation in the CUT&Tag reactions.
+
+![MultiQC - Picard MarkDuplicates metrics plot](images/output/mqc_19_picard_markduplicates.png)
+
+High levels of duplication are not necessarily a problem as long as they are consistent across biological replicates or other comparable groups. Given that the target samples are not de-duplicated by default, if the balance of duplicate reads is off when comparing two samples, it may lead to inaccurate peak calling and subsequent spurious signals. High levels of non-optical duplication are indicative of over-amplified samples.
+
+## 5. <a name='Fragment-basedQC'></a>Fragment-based QC
+
+This section of the pipeline deals with quality control at the aligned fragment level. The read fragments are counted by binning them into regions genome-wide. The default is 500 b.p. but this can be changed using `dt_qc_bam_binsize`. All of the plots shown below are calculated from this initial binned data-set.
+
+### 5.1. <a name='PCA'></a>PCA
+
+Descriptions taken from the deepTools [manual]([plotFingerprint — deepTools 3.5.0 documentation](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
+
+Principal component analysis (PCA) can be used, for example, to determine whether samples display greater variability between experimental conditions than between replicates of the same treatment. PCA is also useful to identify unexpected patterns, such as those caused by batch effects or outliers. Principal components represent the directions along which the variation in the data is maximal, so that the information from thousands of regions can be represented by just a few dimensions.
+
+![plot](images/output/deeptools_pca_plot.png)
+
+### 5.2. <a name='Fingerprint'></a>Fingerprint
+
+Descriptions taken from the deepTools [manual](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html)
+
+This tool is based on a method developed by [Diaz et al.](http://www.ncbi.nlm.nih.gov/pubmed/22499706). It determines how well the signal in the CUT&RUN/Tag sample can be differentiated from the background distribution of reads in the control sample. For factors that exhibit enrichment of well-defined and relatively narrow regions (e.g. transcription factors such as p300), the resulting plot can be used to assess the strength of a CUT&RUN experiment. However, when broad regions of enrichment are to be expected, the less clear the plot will be. Vice versa, if you do not know what kind of signal to expect, the fingerprint plot will give you a straight-forward indication of how careful you will have to be during your downstream analyses to separate noise from meaningful biological signal.
+
+![plot](images/output/deeptools_fingerprint_plot.png)
+
+![plot](images/output/deeptools_fingerprint_explan.png)
+
+### 5.3. <a name='Correlation'></a>Correlation
+
+Descriptions taken from the deepTools [manual](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html)
+
+Computes the overall similarity between two or more samples based on read coverage within genomic regions. The result of the correlation computation is a table of correlation coefficients that indicates how “strong” the relationship between two samples is (values are between -1 and 1: -1 indicates perfect anti-correlation, 1 perfect correlation.)
+
+![plot](images/output/deeptools_correlation_plot.png)
 
-## Peak Calling
+## 6. <a name='PeakCalling'></a>Peak Calling
 
-### Bam to bedgraph
+### 6.1. <a name='Bamtobedgraph'></a>Bam to bedgraph
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -166,9 +297,7 @@ If your data includes IgG controls, these will additionally be de-duplicated. It
 
 Converts bam files to the bedgraph format.
 
-### Clip bedfiles
-
-### Bed to bigwig
+### 6.2. <a name='Bedtobigwig'></a>Bed to bigwig
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -180,107 +309,96 @@ Converts bam files to the bedgraph format.
 
 The [bigWig](https://genome.ucsc.edu/goldenpath/help/bigWig.html) format is an indexed binary format useful for displaying dense, continuous data in Genome Browsers such as the [UCSC](https://genome.ucsc.edu/cgi-bin/hgTracks) and [IGV](http://software.broadinstitute.org/software/igv/). This mitigates the need to load the much larger BAM files for data visualisation purposes which will be slower and result in memory issues. The bigWig format is also supported by various bioinformatics software for downstream processing such as meta-profile plotting.
 
-### SEACR peak calling
+### 6.3. <a name='SEACRpeakcalling'></a>SEACR peak calling
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `03_peak_calling/04_called_peaks/`
-  - `.peaks*.bed`: BED file containing peak coordinates and peak signal.
+  - BED file containing peak coordinates and peak signal.
 
 </details>
 
-[SEACR](https://github.com/FredHutch/SEACR) is a peak caller for data with low background-noise, so is well suited to CUT&Run/CUT&Tag data. SEACR can take in IgG control bedGraph files in order to avoid calling peaks in regions of the experimental data for which the IgG control is enriched. If `--igg_control false` is specified, SEACR calls enriched regions in target data by selecting the top 5% of regions by AUC by default. This threshold can be overwritten using `--peak_threshold`.
+[SEACR](https://github.com/FredHutch/SEACR) is a peak caller for data with low background-noise, so is well suited to CUT&Run/CUT&Tag data. SEACR can take in IgG control bedGraph files in order to avoid calling peaks in regions of the experimental data for which the IgG control is enriched. If `--use_control false` is specified, SEACR calls enriched regions in target data by selecting the top 5% of regions by AUC by default. This threshold can be overwritten using `--seacr_peak_threshold`.
 
-![Python reporting - peaks reproduced](images/py_reproduced_peaks.png)
+### 6.4. <a name='MACS2peakcalling'></a>MACS2 peak calling
 
-![Python reporting - aligned fragments within peaks](images/py_frags_in_peaks.png)
+- `03_peak_calling/04_called_peaks/`
+  - BED file containing peak coordinates and peak signal.
 
-### Bedtools
+MACS2 is a peak caller used in many other experiments such as ATAC-seq and ChIP-seq. It can deal with high levels of background noise but is generally less sensitive than SEACR. If you are having trouble calling peaks in SEACR, we recommend switching to this peak caller, especially if your QC is saying that you have a high level of background noise.
 
-<details markdown="1">
-<summary>Output files</summary>
+MACS2 has its main parameters exposed through the pipeline configuration. The default p-values and genome size can be changed using the `--macs2_pvalue` and `--macs2_gsize` parameters. MACS2 has two calling modes: narrow and broad peak. We recommend using broad peak for epitopes with a wide peak range such as histone marks, and narrow peak for small binding proteins such as transcription factors. This mode can be changed using `--macs2_narrow_peak`.
 
-- `seacr/`
-  - `{group}.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across replicates within groups
-  - `all_peaks.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across all samples
-- `seacr/consensus_peaks`
-  - `{group}.consensus.peaks.bed`: BED containing consensus peaks for each group
-  - `all_peaks.consensus.peaks.bed`: BED containing consensus peaks across all samples
+### 6.5. <a name='ConsensusPeaks'></a>Consensus Peaks
 
 </details>
 
-The merge function from [BEDtools](https://github.com/arq5x/bedtools2) is used to merge replicate peaks of the same experimental group to create a consensus peak set. This can then optionally be filtered for consensus peaks contributed to be a threshold number of replicates using `--replicate_threshold`. Additionally, the same workflow is run merging across all samples.
+The merge function from [BEDtools](https://github.com/arq5x/bedtools2) is used to merge replicate peaks of the same experimental group to create a consensus peak set. This can then optionally be filtered for consensus peaks contributed to be a threshold number of replicates using `--replicate_threshold`.
 
-![Peak calling - group consensus peak plot](images/consensus_peaks.png)
-![Peak calling - group consensus peak plot](images/all_consensus_peaks.png)
+## 7. <a name='Peak-basedQC'></a>Peak-based QC
 
-## Reporting
+Once the peak calling process is complete, we run a separate set of reports that analyse the quality of the results at the peak level.
 
-### Python reporting
+### 7.1. <a name='PeakCounts'></a>Peak Counts
 
-<details markdown="1">
-<summary>Output files</summary>
+For both the sample peaks and the consensus peaks, a simple count is taken. At the sample level, it is important to see consistency between peak counts of biological replicates. It is the first indicator of whether you replicates samples agree with each other after all of the processing has completed. If you use the consensus peaks and use a replicate threshold of more than 1, it is also important to see how many of your peaks across replicates have translated into consensus peaks.
 
-- `04_reporting/qc/`
-  - `report.pdf`: PDF report of all plots.
-  - `*.png`: individual plots featured in the PDF report.
-  - `*.csv`: corresponding data used to produce the plot.
+In the image below we see comparable peak counts for the H3K27me3 dataset, but a large disparity for the H3K4me3.
 
-</details>
+![plot](images/output/mqc_20_primary_peakcounts.png)
 
-Additional QC and analysis pertaining particularly to CUT&Run and CUT&Tag data are reported in this module. This report was adapted in python from the original CUT&Tag analysis [protocol](https://yezhengstat.github.io/CUTTag_tutorial/) from the [Henikoff Lab](https://research.fredhutch.org/henikoff/en.html).
+### 7.2. <a name='PeakReproducibility'></a>Peak Reproducibility
 
-![Python reporting - fragment length distribution](images/py_frag_hist.png)
+The peak reproducibility report intersects all samples within a group using `bedtools intersect` with a minimum overlap controlled by `min_peak_overlap`. This report is useful along with the peak count report for estimating how reliable the peaks called are between your biological replicates.
 
-### MultiQC
+For example, in the image below when combined with the peak count information we see that although the H3K27me3 replicates both have similar peak counts, < 30% of the peaks are replicated across the replicate set. For H3K4me3, we see that replicate 1 has a small number of peaks called, but that almost 100% of those peaks are replicated in the second replicate. Replicate 2 has < 20% of its replicates reproduced in replicate 1 but by looking at the peak counts we can see this is due to the low number of peaks called.
 
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
+![plot](images/output/mqc_22_primary_peakrepro.png)
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+### 7.3. <a name='FRiPScore'></a>FRiP Score
 
-<details markdown="1">
-<summary>Output files</summary>
+Fraction of fragments in peaks (FRiP), defined as the fraction of all mapped paired-end reads extended into fragments that fall into the called peak regions, i.e. usable fragments in significantly enriched peaks divided by all usable fragments. In general, FRiP scores correlate positively with the number of regions. (Landt et al, Genome Research Sept. 2012, 22(9): 1813–1831). A minimum overlap is controlled by `min_frip_overlap`. The FRiP score can be used to assess the overall quality of a sample. Poor samples with a high level of background noise, small numbers of called peaks or other issues will have a large number of fragments falling outside the peaks that were called. Generally FRiP scores > 0.3 are considered to be reasonable with the highest quality data having FRiP scores of > 0.7.
 
-- `04_reporting/multiqc/`
-  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
+It is worth noting that the peak caller settings are also crucial to this score, as even the highest quality data will have a low FRiP score if the pipeline is parameterised in a way that calls few peaks, such as setting the peak calling threshold very high.
 
-</details>
+## 8. <a name='FragmentLengthDistribution'></a>Fragment Length Distribution
 
-### IGV
+CUT&Tag inserts adapters on either side of chromatin particles in the vicinity of the tethered enzyme, although tagmentation within chromatin particles can also occur. So, CUT&Tag reactions targeting a histone modification predominantly results in fragments that are nucleosomal lengths (~180 bp), or multiples of that length. CUT&Tag targeting transcription factors predominantly produce nucleosome-sized fragments and variable amounts of shorter fragments, from neighbouring nucleosomes and the factor-bound site, respectively. Tagmentation of DNA on the surface of nucleosomes also occurs, and plotting fragment lengths with single-basepair resolution reveal a 10-bp sawtooth periodicity, which is typical of successful CUT&Tag experiments.
 
-<details markdown="1">
-<summary>Output files</summary>
+**NB:** Experiments targeting transcription factors may produce different fragment distributions depending on factors beyond the scope of this article.
 
-- `04_reporting/igv/`
-  - `igv_session.xml`: IGV session.
-  - `*.txt`: IGV input file configurations.
+![plot](images/output/mqc_21_fragment_lengths.png)
 
-</details>
+### 8.1. <a name='Heatmaps'></a>Heatmaps
 
-An IGV session file will be created at the end of the pipeline containing the normalised bigWig tracks, per-sample peaks, target genome fasta and annotation GTF. Once installed, open IGV, go to File > Open Session and select the igv_session.xml file for loading.
+Heatmaps for both genomic features and peaks are generated using deepTools. The parameters for the gene heatmap generation including kilobases to map before and after the gene body can be found with the prefix `dt_heatmap_gene_*`. Similarly, the peak-based heatmap parameters can be found using `dt_heatmap_peak_*`.
 
-> **NB:** If you are not using an in-built genome provided by IGV you will need to load the annotation yourself e.g. in .gtf and/or .bed format.
+**NB:** These reports are generated outside of MultiQC
 
-### Deeptools
+![plot](images/output/deeptools_heatmap.png)
 
-<details markdown="1">
-<summary>Output files</summary>
+### 8.2. <a name='UpsetPlots'></a>Upset Plots
+
+Upset plots provide a different view on which sets of peaks are overlapping across different samples. Use in conjunction with the other peak-based QC metrics.
+
+**NB:** These reports are generated outside of MultiQC
 
-- `04_reporting/heatmaps/<gene/peak>/`
-  - `.plotHeatmap.pdf`: heatmap PDF.
-  - `.computeMatrix.mat.gz`: heatmap matrix.
-  - `*.mat.tab`: matrix and heatmap configs.
+![plot](images/output/all_consensus_peaks.png)
 
 </details>
 
-[deeptools](https://github.com/deeptools/deepTools/) sub-tools computeMatrix and plotHeatmap are used to assess the distribution of fragments around genes and peaks.
+### 8.3. <a name='IGV'></a>IGV
+
+</details>
+
+An IGV session file will be created at the end of the pipeline containing the normalised bigWig tracks, per-sample peaks, target genome fasta and annotation GTF. Once installed, open IGV, go to File > Open Session and select the `igv_session.xml` file for loading.
+
+> **NB:** If you are not using an in-built genome provided by IGV you will need to load the annotation yourself e.g. in .gtf and/or .bed format.
 
-## Workflow reporting and genomes
+## 9. <a name='Workflowreportingandgenomes'></a>Workflow reporting and genomes
 
-### Reference genome files
+### 9.1. <a name='Referencegenomefiles'></a>Reference genome files
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -296,7 +414,7 @@ An IGV session file will be created at the end of the pipeline containing the no
 
 A number of genome-specific files are generated by the pipeline because they are required for the downstream processing of the results. If the `--save_reference` parameter is provided then these will be saved in the `00_genome/` directory. It is recommended to use the `--save_reference` parameter if you are using the pipeline to build new indices so that you can save them somewhere locally. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space.
 
-### Pipeline information
+### 9.2. <a name='Pipelineinformation'></a>Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>
diff --git a/docs/usage.md b/docs/usage.md
index 7f9b91cb..f9699e06 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -46,9 +46,9 @@ This will launch the pipeline with the `docker` configuration profile. See below
 
 Note that the pipeline will create the following files in your working directory:
 
-```console
+```bash
 work                # Directory containing the nextflow working files
-<OUTIDR>            # Finished results in specified location (defined with --outdir)
+<OUTDIR>            # Finished results in specified location (defined with --outdir)
 .nextflow_log       # Log file from Nextflow
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
@@ -57,7 +57,7 @@ work                # Directory containing the nextflow working files
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
-```console
+```bash
 nextflow pull nf-core/cutandrun
 ```
 
@@ -67,7 +67,29 @@ nextflow pull nf-core/cutandrun
 
 There are some options detailed on the parameters page that are prefixed with `save`, `skip` or `only`. These are flow control options that allow for saving additional output to the results directory, skipping unwanted portions of the pipeline or running the pipeline up to a certain point, which can be useful for testing.
 
-### De-duplication
+### Genome Configuration
+
+The easiest way to run the pipeline is by using one of the pre-configured genomes that reflect the available genomes at [iGenomes]([AWS iGenomes](https://ewels.github.io/AWS-iGenomes/)). Assign `genome` to one of the key words for iGenomes and all the available reference data will be automatically fetched. The pipeline uses the following reference data:
+
+- Target genome FASTA
+
+- Target genome Bowtie2 Index
+
+- Target genome GTF
+
+- Target genome BED (will be generated from the GTF if not supplied)
+
+- Target genome Blacklist (blacklist files for major genomes are included in the pipeline)
+
+- Spike-in genome FASTA
+
+- Spike-in genome Bowtie2 Index
+
+If the `genome` parameter is not supplied, the user must provide all the target genome data themselves (except the gene BED file). The default spike-in genome is e.coli given that this is the natural spike-in product of the protein production process. However, it is possible to spike-in different DNA during the experimental protocol and then set the `spikein_genome` to the target organism.
+
+### Read Filtering and Duplication
+
+After alignment using Bowtie2, mapped reads are filtered to remove those which do not pass a minimum quality threshold. This threshold can be changed using the `minimum_alignment_q_score` parameter.
 
 CUT&RUN and CUT&Tag both integrate adapters into the vicinity of antibody-tethered enzymes, and the exact sites of integration are affected by the accessibility of surrounding DNA. Given these experimental parameters, it is expected that there are many fragments which share common starting and end positions; thus, such duplicates are generally valid but would be filtered out by de-duplication tools. However, there will be a fraction of fragments that are present due to PCR duplication that cannot be separated.
 
@@ -75,9 +97,9 @@ Control samples such as those from IgG datasets have relatively high duplication
 
 The default for the pipeline therefore is to only run de-duplication on control samples. If it is suspected that there is a heavy fraction of PCR duplicates present in the primary samples then the parameter `dedup_target_reads` can be set using
 
-`--dedup_target_reads true`
+`--dedup_target_reads`
 
-### Peak Normalisation
+### Read Normalisation
 
 The default mode in the pipeline is to normalise stacked reads before peak calling for epitope abundance using spike-in normalisation.
 
@@ -264,6 +286,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
+## Azure Resource Requests
+
+To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
+We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
+
+Note that the choice of VM size depends on your quota and the overall workload during the analysis.
+For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
+
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
@@ -278,6 +308,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo
 In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
 We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
 
-```console
+```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 2fc0a9b9..27feb009 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -145,6 +145,61 @@ class NfcoreTemplate {
         output_tf.withWriter { w -> w << email_txt }
     }
 
+    //
+    // Construct and send adaptive card
+    // https://adaptivecards.io
+    //
+    public static void adaptivecard(workflow, params, summary_params, projectDir, log) {
+        def hook_url = params.hook_url
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['start']                                = workflow.start
+        misc_fields['complete']                             = workflow.complete
+        misc_fields['scriptfile']                           = workflow.scriptFile
+        misc_fields['scriptid']                             = workflow.scriptId
+        if (workflow.repository) misc_fields['repository']  = workflow.repository
+        if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
+        if (workflow.revision)   misc_fields['revision']    = workflow.revision
+        misc_fields['nxf_version']                          = workflow.nextflow.version
+        misc_fields['nxf_build']                            = workflow.nextflow.build
+        misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+
+        def msg_fields = [:]
+        msg_fields['version']      = workflow.manifest.version
+        msg_fields['runName']      = workflow.runName
+        msg_fields['success']      = workflow.success
+        msg_fields['dateComplete'] = workflow.complete
+        msg_fields['duration']     = workflow.duration
+        msg_fields['exitStatus']   = workflow.exitStatus
+        msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        msg_fields['commandLine']  = workflow.commandLine
+        msg_fields['projectDir']   = workflow.projectDir
+        msg_fields['summary']      = summary << misc_fields
+
+        // Render the JSON template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def hf = new File("$projectDir/assets/adaptivecard.json")
+        def json_template = engine.createTemplate(hf).make(msg_fields)
+        def json_message  = json_template.toString()
+
+        // POST
+        def post = new URL(hook_url).openConnection();
+        post.setRequestMethod("POST")
+        post.setDoOutput(true)
+        post.setRequestProperty("Content-Type", "application/json")
+        post.getOutputStream().write(json_message.getBytes("UTF-8"));
+        def postRC = post.getResponseCode();
+        if (! postRC.equals(200)) {
+            log.warn(post.getErrorStream().getText());
+        }
+    }
+
     //
     // Print pipeline summary on completion
     //
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
old mode 100755
new mode 100644
index 28567bd7..8d030f4e
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -21,19 +21,26 @@ class Utils {
         }
 
         // Check that all channels are present
-        def required_channels = ['conda-forge', 'bioconda', 'defaults']
-        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+        // This channel list is ordered by required channel priority.
+        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+        def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order
-        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
-        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+        def channel_priority_violation = false
+        def n = required_channels_in_order.size()
+        for (int i = 0; i < n - 1; i++) {
+            channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+        }
 
-        if (conda_check_failed) {
+        if (channels_missing | channel_priority_violation) {
             log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
                 "  There is a problem with your Conda configuration!\n\n" +
                 "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
-                "  NB: The order of the channels matters!\n" +
+                "  Please refer to https://bioconda.github.io/\n" +
+                "  The observed channel order is \n" +
+                "  ${channels}\n" +
+                "  but the following channel order is required:\n" +
+                "  ${required_channels_in_order}\n" +
                 "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         }
     }
diff --git a/lib/WorkflowCutandrun.groovy b/lib/WorkflowCutandrun.groovy
index fc19f68a..35ce645e 100755
--- a/lib/WorkflowCutandrun.groovy
+++ b/lib/WorkflowCutandrun.groovy
@@ -2,6 +2,8 @@
 // This file holds several functions specific to the workflow/cutandrun.nf in the nf-core/cutandrun pipeline
 //
 
+import groovy.text.SimpleTemplateEngine
+
 class WorkflowCutandrun {
 
     //
@@ -10,6 +12,7 @@ class WorkflowCutandrun {
     public static void initialise(params, log) {
         genomeExistsError(params, log)
 
+
         if (!params.fasta) {
             log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
             System.exit(1)
@@ -62,7 +65,22 @@ class WorkflowCutandrun {
         return yaml_file_text
     }
 
-    //
+    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+        def meta = [:]
+        meta.workflow = run_workflow.toMap()
+        meta["manifest_map"] = run_workflow.manifest.toMap()
+
+        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
+    }//
     // Exit pipeline if incorrect --genome key provided
     //
     private static void genomeExistsError(params, log) {
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 87df6453..4891ba4d 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -57,6 +57,7 @@ class WorkflowMain {
         }
 
         // Print parameter summary log to screen
+
         log.info paramsSummaryLog(workflow, params, log)
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
@@ -76,18 +77,16 @@ class WorkflowMain {
             System.exit(1)
         }
     }
-
     //
     // Get attribute from genome config file e.g. fasta
     //
-    public static String getGenomeAttribute(params, attribute) {
-        def val = ''
+    public static Object getGenomeAttribute(params, attribute) {
         if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
             if (params.genomes[ params.genome ].containsKey(attribute)) {
-                val = params.genomes[ params.genome ][ attribute ]
+                return params.genomes[ params.genome ][ attribute ]
             }
         }
-        return val
+        return null
     }
 
     //
diff --git a/main.nf b/main.nf
index bb4380e2..4f2732c4 100644
--- a/main.nf
+++ b/main.nf
@@ -4,6 +4,7 @@
     nf-core/cutandrun
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/nf-core/cutandrun
+
     Website: https://nf-co.re/cutandrun
     Slack  : https://nfcore.slack.com/channels/cutandrun
 ----------------------------------------------------------------------------------------
@@ -17,13 +18,8 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-if (!params.fasta) {
-    params.bowtie2   = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
-} else {
-    params.bowtie2   = null
-}
-
 params.fasta     = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.bowtie2   = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
 params.gtf       = WorkflowMain.getGenomeAttribute(params, 'gtf')
 params.gene_bed  = WorkflowMain.getGenomeAttribute(params, 'bed12')
 params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
@@ -34,12 +30,8 @@ params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
 ========================================================================================
 */
 
-if (!params.spikein_fasta) {
-    params.spikein_bowtie2 = WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
-} else {
-    params.spikein_bowtie2 = null
-}
 params.spikein_fasta   = WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')
+params.spikein_bowtie2 = WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/modules.json b/modules.json
index 4f20b9e8..6ad04247 100644
--- a/modules.json
+++ b/modules.json
@@ -2,81 +2,118 @@
     "name": "nf-core/cutandrun",
     "homePage": "https://github.com/nf-core/cutandrun",
     "repos": {
-        "nf-core/modules": {
-            "bedtools/bamtobed": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "bedtools/genomecov": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "bedtools/intersect": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "bedtools/merge": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "bedtools/sort": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "bowtie2/align": {
-                "git_sha": "cbc47767f7bb4751a9d178395bd66f051401a0c1"
-            },
-            "bowtie2/build": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "cat/fastq": {
-                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
-            },
-            "custom/getchromsizes": {
-                "git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08"
-            },
-            "deeptools/computematrix": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "deeptools/plotheatmap": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "fastqc": {
-                "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
-            },
-            "gunzip": {
-                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
-            },
-            "macs2/callpeak": {
-                "git_sha": "f0800157544a82ae222931764483331a81812012"
-            },
-            "picard/markduplicates": {
-                "git_sha": "63db63757cab03cfa7a02c0d0f134b66fbfadea6"
-            },
-            "samtools/flagstat": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
-            },
-            "samtools/idxstats": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
-            },
-            "samtools/index": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
-            },
-            "samtools/sort": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
-            },
-            "samtools/stats": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
-            },
-            "samtools/view": {
-                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
-            },
-            "seacr/callpeak": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "ucsc/bedclip": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "ucsc/bedgraphtobigwig": {
-                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
-            },
-            "untar": {
-                "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "bedtools/bamtobed": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bedtools/complement": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bedtools/genomecov": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bedtools/intersect": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bedtools/merge": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bowtie2/align": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "bowtie2/build": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "cat/fastq": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "custom/getchromsizes": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "deeptools/computematrix": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "deeptools/plotfingerprint": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "deeptools/plotheatmap": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "macs2/callpeak": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "picard/markduplicates": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/flagstat": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/idxstats": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/sort": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/stats": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "seacr/callpeak": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "tabix/bgziptabix": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "ucsc/bedclip": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "ucsc/bedgraphtobigwig": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    }
+                }
             }
         }
     }
diff --git a/modules/local/modules/custom/dumpsoftwareversions/main.nf b/modules/local/custom_dumpsoftwareversions.nf
similarity index 89%
rename from modules/local/modules/custom/dumpsoftwareversions/main.nf
rename to modules/local/custom_dumpsoftwareversions.nf
index ddc7306d..ad1626e2 100644
--- a/modules/local/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/local/custom_dumpsoftwareversions.nf
@@ -1,8 +1,8 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.12" : null)
+    conda (params.enable_conda ? "bioconda::multiqc=1.13" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
@@ -127,8 +127,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     }
 
     versions_mqc = {
-        'id': 'software_versions',
-        'section_name': '${workflow.manifest.name} Software Versions by Process',
+        'parent_id': 'software_versions',
+        'parent_name': 'Software Versions',
+        'parent_description': 'Details software versions used in the pipeline run',
+        'id': 'software-versions-by-process',
+        'section_name': '${workflow.manifest.name} software versions by process',
         'section_href': 'https://github.com/${workflow.manifest.name}',
         'plot_type': 'html',
         'description': 'are collected at run time from the software output.',
@@ -136,7 +139,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     }
 
     versions_mqc_unique = {
-        'id': 'software_versions_unique',
+        'parent_id': 'software_versions',
+        'parent_name': 'Software Versions',
+        'parent_description': 'Details software versions used in the pipeline run',
+        'id': 'software-versions-unique',
         'section_name': '${workflow.manifest.name} Software Versions',
         'section_href': 'https://github.com/${workflow.manifest.name}',
         'plot_type': 'html',
diff --git a/modules/local/modules/deeptools/bamcoverage/main.nf b/modules/local/deeptools/bamcoverage/main.nf
similarity index 100%
rename from modules/local/modules/deeptools/bamcoverage/main.nf
rename to modules/local/deeptools/bamcoverage/main.nf
diff --git a/modules/local/deeptools/multibamsummary/main.nf b/modules/local/deeptools/multibamsummary/main.nf
new file mode 100644
index 00000000..d6fe03ec
--- /dev/null
+++ b/modules/local/deeptools/multibamsummary/main.nf
@@ -0,0 +1,35 @@
+process DEEPTOOLS_MULTIBAMSUMMARY {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' :
+        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(bams), path(bais), val(labels)
+
+    output:
+    tuple val(meta), path("*.npz") , emit: matrix
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    multiBamSummary bins \\
+        $args \\
+        --bamfiles ${bams.join(' ')} \\
+        --labels ${labels.join(' ')} \\
+        --numberOfProcessors $task.cpus \\
+        --outFileName all_bam.bamSummary.npz \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(multiBamSummary --version | sed -e "s/multiBamSummary //g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/deeptools/plotcorrelation/main.nf b/modules/local/deeptools/plotcorrelation/main.nf
new file mode 100644
index 00000000..546a0ad7
--- /dev/null
+++ b/modules/local/deeptools/plotcorrelation/main.nf
@@ -0,0 +1,36 @@
+process DEEPTOOLS_PLOTCORRELATION {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' :
+        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(matrix)
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.tab"), emit: matrix
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    plotCorrelation \\
+        $args \\
+        --corData $matrix \\
+        --plotFile ${prefix}.plotCorrelation.pdf \\
+        --outFileCorMatrix ${prefix}.plotCorrelation.mat.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(plotCorrelation --version | sed -e "s/plotCorrelation //g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/deeptools/plotpca/main.nf b/modules/local/deeptools/plotpca/main.nf
new file mode 100644
index 00000000..a2193183
--- /dev/null
+++ b/modules/local/deeptools/plotpca/main.nf
@@ -0,0 +1,36 @@
+process DEEPTOOLS_PLOTPCA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' :
+        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(matrix)
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.tab"), emit: tab
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    plotPCA \\
+        $args \\
+        --corData $matrix \\
+        --plotFile ${prefix}.plotPCA.pdf \\
+        --outFileNameData ${prefix}.plotPCA.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(plotPCA --version | sed -e "s/plotPCA //g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/export_meta.nf b/modules/local/export_meta.nf
deleted file mode 100644
index 6a18e362..00000000
--- a/modules/local/export_meta.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process EXPORT_META {
-    label 'process_min'
-
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
-
-    input:
-    val meta
-    val table_name
-
-    output:
-    path "*.csv", emit: csv
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def header = [:]
-
-    // Find the header key set
-    for (int i = 0; i < meta.size(); i++) {
-        meta[i].each {
-            entry ->
-                if(!header.containsKey(entry.key)) {
-                    header.put(entry.key, null)
-                }
-        }
-    }
-
-    // Init output string
-    arr_str = header.keySet().join(",")
-
-    // Map the values and write row
-    for (int i = 0; i < meta.size(); i++) {
-        header.each {
-            entry ->
-                entry.value = null
-        }
-
-        meta[i].each {
-            entry ->
-                header[entry.key] = entry.value
-        }
-        sample_str = header.values().join(",")
-        arr_str =  arr_str + "\n" + sample_str
-    }
-
-    """
-    echo "$arr_str" > ${table_name}.csv
-    """
-}
diff --git a/modules/nf-core/modules/bedtools/sort/main.nf b/modules/local/for_patch/bedtools/sort/main.nf
similarity index 89%
rename from modules/nf-core/modules/bedtools/sort/main.nf
rename to modules/local/for_patch/bedtools/sort/main.nf
index 43dc9bda..e4d47183 100644
--- a/modules/nf-core/modules/bedtools/sort/main.nf
+++ b/modules/local/for_patch/bedtools/sort/main.nf
@@ -10,6 +10,7 @@ process BEDTOOLS_SORT {
     input:
     tuple val(meta), path(intervals)
     val   extension
+    path  sizes
 
     output:
     tuple val(meta), path("*.${extension}"), emit: sorted
@@ -19,12 +20,14 @@ process BEDTOOLS_SORT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def sizes  = sizes ? "-g $sizes" : ""
     """
     bedtools \\
         sort \\
         -i $intervals \\
+        $sizes \\
         $args \\
         > ${prefix}.${extension}
 
diff --git a/modules/nf-core/modules/bedtools/sort/meta.yml b/modules/local/for_patch/bedtools/sort/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bedtools/sort/meta.yml
rename to modules/local/for_patch/bedtools/sort/meta.yml
diff --git a/modules/local/for_patch/preseq/lcextrap/main.nf b/modules/local/for_patch/preseq/lcextrap/main.nf
new file mode 100644
index 00000000..cf76779b
--- /dev/null
+++ b/modules/local/for_patch/preseq/lcextrap/main.nf
@@ -0,0 +1,40 @@
+process PRESEQ_LCEXTRAP {
+    tag "$meta.id"
+    label 'process_medium'
+    label 'error_ignore'
+
+    conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
+        'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap, optional:true
+    tuple val(meta), path("*.log")          , emit: log
+    path  "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def paired_end = meta.single_end ? '' : '-pe'
+    """
+    preseq \\
+        lc_extrap \\
+        $args \\
+        $paired_end \\
+        -output ${prefix}.lc_extrap.txt \\
+        $bam \\
+    && cp .command.log ${prefix}.command.log || cp .command.log ${prefix}.command.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/for_patch/preseq/lcextrap/meta.yml b/modules/local/for_patch/preseq/lcextrap/meta.yml
new file mode 100755
index 00000000..f1be05a2
--- /dev/null
+++ b/modules/local/for_patch/preseq/lcextrap/meta.yml
@@ -0,0 +1,48 @@
+name: preseq_lcextrap
+description: Software for predicting library complexity and genome coverage in high-throughput sequencing
+keywords:
+  - preseq
+  - library
+  - complexity
+tools:
+  - preseq:
+      description: Software for predicting library complexity and genome coverage in high-throughput sequencing
+      homepage: http://smithlabresearch.org/software/preseq/
+      documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
+      tool_dev_url: https://github.com/smithlabcode/preseq
+      doi: ""
+      licence: ["GPL"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - lc_extrap:
+      type: file
+      description: File containing output of Preseq lcextrap
+      pattern: "*.{lc_extrap.txt}"
+  - log:
+      type: file
+      description: Log file containing stderr produced by Preseq
+      pattern: "*.{log}"
+
+authors:
+  - "@drpatelh"
+  - "@Emiller88"
diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/local/for_patch/samtools/view/main.nf
similarity index 95%
rename from modules/nf-core/modules/samtools/view/main.nf
rename to modules/local/for_patch/samtools/view/main.nf
index 55194e88..b05e8aac 100644
--- a/modules/nf-core/modules/samtools/view/main.nf
+++ b/modules/local/for_patch/samtools/view/main.nf
@@ -10,6 +10,7 @@ process SAMTOOLS_VIEW {
     input:
     tuple val(meta), path(input), path(index)
     path fasta
+    path regions
 
     output:
     tuple val(meta), path("*.bam") , emit: bam , optional: true
@@ -24,6 +25,7 @@ process SAMTOOLS_VIEW {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta} -C" : ""
+    def blacklist = regions ? "-L $regions" : ""
     def file_type = input.getExtension()
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
@@ -31,6 +33,7 @@ process SAMTOOLS_VIEW {
         view \\
         --threads ${task.cpus-1} \\
         ${reference} \\
+        ${blacklist} \\
         $args \\
         $input \\
         $args2 \\
diff --git a/modules/nf-core/modules/samtools/view/meta.yml b/modules/local/for_patch/samtools/view/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/view/meta.yml
rename to modules/local/for_patch/samtools/view/meta.yml
diff --git a/modules/local/modules/trimgalore/main.nf b/modules/local/for_patch/trimgalore/main.nf
similarity index 100%
rename from modules/local/modules/trimgalore/main.nf
rename to modules/local/for_patch/trimgalore/main.nf
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
new file mode 100644
index 00000000..a6540ad1
--- /dev/null
+++ b/modules/local/gtf2bed.nf
@@ -0,0 +1,32 @@
+process GTF2BED {
+    tag "$gtf"
+    label 'process_low'
+
+    conda (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
+        'quay.io/biocontainers/perl:5.26.2' }"
+
+    input:
+    path gtf
+
+    output:
+    path '*.bed'       , emit: bed
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script: // This script is bundled with the pipeline, in nf-core/cutandrun/bin/
+    def args = params.igv_show_gene_names ? "--names" : ''
+    """
+    gtf2bed \\
+        $args \\
+        $gtf \\
+        > ${gtf.baseName}.bed
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/linux/awk.nf b/modules/local/linux/awk.nf
index d56926f9..ad2f299d 100644
--- a/modules/local/linux/awk.nf
+++ b/modules/local/linux/awk.nf
@@ -1,6 +1,6 @@
 process AWK {
     tag "$meta.id"
-    label 'process_ultralow'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/linux/cut.nf b/modules/local/linux/cut.nf
index 1afaedc2..da921d03 100644
--- a/modules/local/linux/cut.nf
+++ b/modules/local/linux/cut.nf
@@ -1,6 +1,6 @@
 process CUT {
     tag "$meta.id"
-    label 'process_min'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/modules/calculate_frip/main.nf b/modules/local/modules/calculate_frip/main.nf
deleted file mode 100644
index 0a7d2d8f..00000000
--- a/modules/local/modules/calculate_frip/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-process CALCULATE_FRIP {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda (params.enable_conda ? "conda-forge::python=3.8.3 bioconda::deeptools=3.5.* bioconda::pysam=0.17.*" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :
-        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"
-
-    input:
-    tuple val(meta), path(bam), path(bai), path(bed)
-
-    output:
-    tuple val(meta), path('frips.csv'), emit: frips
-    path  "versions.yml"              , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    """
-    frip.py \\
-        --bams "*.bam" \\
-        --peaks "*.bed" \\
-        --threads ${task.cpus} \\
-        --outpath .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | grep -E -o \"([0-9]{1,}\\.)+[0-9]{1,}\")
-        deeptools: \$(deeptools --version | sed -e "s/deeptools //g")
-        pysam: \$(python -c 'import pysam; print(pysam.__version__)')
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/modules/custom/dumpsoftwareversions/meta.yml b/modules/local/modules/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index 5ef619d0..00000000
--- a/modules/local/modules/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
diff --git a/modules/local/modules/deeptools/bamcoverage/meta.yml b/modules/local/modules/deeptools/bamcoverage/meta.yml
deleted file mode 100644
index fb92168f..00000000
--- a/modules/local/modules/deeptools/bamcoverage/meta.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: deeptools_bamcoverage
-description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
-keywords:
-  - sort
-tools:
-  - deeptools:
-      description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
-      homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
-      documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
-      tool_dev_url: https://github.com/deeptools/deepTools/
-      doi: "https://doi.org/10.1093/nar/gkw257"
-      licence: ["GPL v3"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM file
-      pattern: "*.{bam,cram}"
-  - input_index:
-      type: file
-      description: BAM/CRAM index file
-      pattern: "*.{bai,crai}"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - bigWig:
-      type: file
-      description: BigWig file
-      pattern: "*.bigWig"
-  - bedgraph:
-      type: file
-      description: Bedgraph file
-      pattern: "*.bedgraph"
-
-authors:
-  - "@FriederikeHanssen"
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 823ee449..803a8bce 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -1,17 +1,17 @@
 process MULTIQC {
-    label 'process_ultralow'
+    label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.12" : null)
+    conda (params.enable_conda ? "bioconda::multiqc=1.13" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path multiqc_config
     path multiqc_custom_config
-    path software_versions
-    path software_versions_unique
-    path workflow_summary
+    path ('software_versions/*')
+    path ('software_versions/*')
+    path ('workflow_summary/*')
     path ('fastqc/*')
     path ('trimgalore/fastqc/*')
     path ('trimgalore/*')
@@ -21,12 +21,21 @@ process MULTIQC {
     path ('samtools/flagstat/*')
     path ('samtools/idxstats/*')
     path ('picard/markduplicates/*')
-    path ('reports/*')
+    path ('preseq/*')
+    path ('deeptools/*')
+    path ('deeptools/*')
+    path ('deeptools/*')
+    path ('peak_metrics/peak_count/*')
+    path ('peak_metrics/peak_frip/*')
+    path ('peak_metrics/peak_count_consensus/*')
+    path ('peak_metrics/peak_reprod_perc/*')
+    path ('frag_len/*')
 
     output:
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
     path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,5 +45,10 @@ process MULTIQC {
     def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
     """
     multiqc -f $args $custom_config .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
     """
 }
diff --git a/modules/local/peak_counts.nf b/modules/local/peak_counts.nf
new file mode 100644
index 00000000..36ce7c60
--- /dev/null
+++ b/modules/local/peak_counts.nf
@@ -0,0 +1,31 @@
+process PEAK_COUNTS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+
+    input:
+    tuple val(meta), path(bed)
+    path  peak_counts_header
+
+    output:
+    tuple val(meta), path("*mqc.tsv"), emit: count_mqc
+    path  "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cat ${bed} | wc -l | awk -v OFS='\t' '{ print "Peak Count", \$1 }' | cat $peak_counts_header - > ${prefix}_mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/peak_frip.nf b/modules/local/peak_frip.nf
new file mode 100644
index 00000000..3a3bbe8b
--- /dev/null
+++ b/modules/local/peak_frip.nf
@@ -0,0 +1,33 @@
+process PEAK_FRIP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+
+    input:
+    tuple val(meta), path(peaks_bed), path(fragments_bed), path(flagstat)
+    path  frip_score_header
+    val   min_frip_overlap
+
+    output:
+    tuple val(meta), path("*mqc.tsv"), emit: frip_mqc
+    path  "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    READS_IN_PEAKS=\$(bedtools intersect -a ${fragments_bed} -b ${peaks_bed} -bed -c -f $min_frip_overlap |  awk -F '\t' '{sum += \$NF} END {print sum * 2}')
+    grep -m 1 'mapped (' ${flagstat} | awk -v a="\$READS_IN_PEAKS" -v OFS='\t' '{print "Peak FRiP Score", a/\$1}' | cat $frip_score_header - > ${prefix}_mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/modules/generate_reports/main.nf b/modules/local/python/frag_len_hist.nf
similarity index 58%
rename from modules/local/modules/generate_reports/main.nf
rename to modules/local/python/frag_len_hist.nf
index 4267d2e9..ccd3f649 100644
--- a/modules/local/modules/generate_reports/main.nf
+++ b/modules/local/python/frag_len_hist.nf
@@ -1,5 +1,5 @@
-process GENERATE_REPORTS {
-    label 'process_ultralow'
+process FRAG_LEN_HIST {
+    label 'process_medium'
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::pandas=1.3.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -7,38 +7,24 @@ process GENERATE_REPORTS {
         'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"
 
     input:
-    path meta_data
-    path meta_data_ctrl
     path raw_fragments
-    path bed_fragments
-    path seacr_beds
     path frag_len_header_multiqc
 
     output:
-    path '*.pdf'             , emit: pdf
-    path '*.csv'             , emit: csv
-    path '*.png'             , emit: png
-    path '*frag_len_mqc.yml', emit: frag_len_multiqc
+    path '*frag_len_mqc.yml', emit: frag_len_mqc
     path  "versions.yml"     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def meta_data_resolved = meta_data ? meta_data : meta_data_ctrl
-
     """
-    reporting.py gen_reports \\
-        --meta $meta_data_resolved \\
-        --meta_ctrl $meta_data_ctrl \\
-        --raw_frag "*.frags.len.txt" \\
-        --bin_frag "*bin500.awk.bed" \\
-        --seacr_bed "*bed*.bed" \\
-        --output . \\
-        --log log.txt
+    calc_frag_hist.py \\
+        --frag_path "*len.txt" \\
+        --output frag_len_hist.txt
 
-    if [ -f "03_03_frag_len_mqc.txt" ]; then
-        cat $frag_len_header_multiqc 03_03_frag_len_mqc.txt > frag_len_mqc.yml
+    if [ -f "frag_len_hist.txt" ]; then
+        cat $frag_len_header_multiqc frag_len_hist.txt > frag_len_mqc.yml
     fi
 
     cat <<-END_VERSIONS > versions.yml
@@ -49,4 +35,4 @@ process GENERATE_REPORTS {
         seaborn: \$(python -c 'import seaborn; print(seaborn.__version__)')
     END_VERSIONS
     """
-}
+}
\ No newline at end of file
diff --git a/modules/local/python/igv_session.nf b/modules/local/python/igv_session.nf
index 275f7cdb..231b28e2 100644
--- a/modules/local/python/igv_session.nf
+++ b/modules/local/python/igv_session.nf
@@ -9,12 +9,15 @@ process IGV_SESSION {
 
     input:
     path genome
-    path gtf
+    path genome_index
+    //path gtf
+    tuple val(meta), path(gtf_bed), path(gtf_bed_index)
     path beds
+    path secondary_beds
     path bigwig
 
     output:
-    path('*.{txt,xml,bed,bigWig,fa,fna,gtf,gff}', includeInputs:true)
+    path('*.{txt,xml,bed,bigWig,fa,fai,fna,gtf,gff,narrowPeak,broadPeak,gz,tbi,bedGraph}', includeInputs:true)
     path  "versions.yml"                , emit: versions
 
     when:
@@ -26,6 +29,7 @@ process IGV_SESSION {
     colour_pos = 0
 
     file_list = beds.collect{it.toString()}.sort()
+    file_list += secondary_beds.collect{it.toString()}.sort()
     file_list += bigwig.collect{it.toString()}.sort()
     for(file in file_list){
         file_split = file.split('_R')
@@ -49,7 +53,7 @@ process IGV_SESSION {
     find -L * -iname "*.gtf" -exec echo -e {}"\\t0,48,73" \\; > gtf.igv.txt
     find -L * -iname "*.gff" -exec echo -e {}"\\t0,48,73" \\; > gff.igv.txt
     cat *.txt > igv_files.txt
-    igv_files_to_session.py igv_session.xml igv_files.txt $genome --path_prefix './'
+    igv_files_to_session.py igv_session.xml igv_files.txt $genome $gtf_bed --path_prefix './'
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/python/merge_sample_metadata.nf b/modules/local/python/merge_sample_metadata.nf
new file mode 100644
index 00000000..038fad8e
--- /dev/null
+++ b/modules/local/python/merge_sample_metadata.nf
@@ -0,0 +1,38 @@
+process MERGE_SAMPLE_METADATA {
+    label 'process_single'
+
+    conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::pandas=1.3.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :
+        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"
+
+    input:
+    path metadata
+
+    output:
+    path '*.csv'             , emit: csv
+    path  "versions.yml"     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def ext             = task.ext.output ?: 'csv'
+    def output          = task.ext.output ?: 'NO_NAME.csv'
+    def id_parse_string = task.ext.id_parse_string ?: ''
+
+    """
+    reports.py merge_samples \\
+        --metadata "*.${ext}" \\
+        --id_parse_string $id_parse_string \\
+        --output $output \\
+        --log log.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | grep -E -o \"([0-9]{1,}\\.)+[0-9]{1,}\")
+        numpy: \$(python -c 'import numpy; print(numpy.__version__)')
+        pandas: \$(python -c 'import pandas; print(pandas.__version__)')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/modules/calculate_peak_reprod/main.nf b/modules/local/python/peak_reprod.nf
similarity index 73%
rename from modules/local/modules/calculate_peak_reprod/main.nf
rename to modules/local/python/peak_reprod.nf
index 11bfea9c..2cdb77ca 100644
--- a/modules/local/modules/calculate_peak_reprod/main.nf
+++ b/modules/local/python/peak_reprod.nf
@@ -1,6 +1,6 @@
 process CALCULATE_PEAK_REPROD {
     tag "$meta.id"
-    label 'process_ultralow'
+    label 'process_medium'
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::dask=2021.9.1 conda-forge::pandas=1.3.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -9,21 +9,28 @@ process CALCULATE_PEAK_REPROD {
 
     input:
     tuple val(meta), path(bed)
+    path peak_reprod_header_multiqc
 
     output:
-    tuple val(meta), path('peak_repro.csv'), emit: csv
-    path  "versions.yml"                   , emit: versions
+    tuple val(meta), path("*peak_repro.tsv"), emit: tsv
+    path "*_mqc.tsv"                        , emit: mqc
+    path  "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
-    peak_reproducability.py \\
+    peak_reproducibility.py \\
+        --sample_id $meta.id \\
         --intersect $bed \\
         --threads ${task.cpus} \\
         --outpath .
 
+    cat $peak_reprod_header_multiqc *peak_repro.tsv > ${prefix}_mqc.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | grep -E -o \"([0-9]{1,}\\.)+[0-9]{1,}\")
diff --git a/modules/local/modules/plot_consensus_peaks/main.nf b/modules/local/python/plot_consensus_peaks.nf
similarity index 95%
rename from modules/local/modules/plot_consensus_peaks/main.nf
rename to modules/local/python/plot_consensus_peaks.nf
index c7fbe474..193ef0ac 100644
--- a/modules/local/modules/plot_consensus_peaks/main.nf
+++ b/modules/local/python/plot_consensus_peaks.nf
@@ -1,5 +1,5 @@
 process PLOT_CONSENSUS_PEAKS {
-    label 'process_min'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -15,7 +15,7 @@ process PLOT_CONSENSUS_PEAKS {
 
     script:
     """
-    consensus_peaks.py \\
+    plot_consensus_peaks.py \\
         --peaks "*.peaks.bed" \\
         --outpath .
 
diff --git a/modules/local/python/samplesheet_check.nf b/modules/local/python/samplesheet_check.nf
index d2aa887c..0ff1a079 100644
--- a/modules/local/python/samplesheet_check.nf
+++ b/modules/local/python/samplesheet_check.nf
@@ -1,6 +1,6 @@
 process SAMPLESHEET_CHECK {
     tag "$samplesheet"
-    label 'process_min'
+    label 'process_single'
 
     conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     container "quay.io/biocontainers/python:3.8.3"
diff --git a/modules/local/samtools_custom_view.nf b/modules/local/samtools_custom_view.nf
index 699c7e03..0540f4e3 100644
--- a/modules/local/samtools_custom_view.nf
+++ b/modules/local/samtools_custom_view.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_CUSTOMVIEW {
     tag "$meta.id"
-    label 'process_ultralow'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -14,6 +14,9 @@ process SAMTOOLS_CUSTOMVIEW {
     tuple val(meta), path("*.txt") , emit: tsv
     path  "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args     = task.ext.args ?: ''
     def args2    = task.ext.args2 ?: ''
diff --git a/modules/nf-core/modules/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf
similarity index 97%
rename from modules/nf-core/modules/bedtools/bamtobed/main.nf
rename to modules/nf-core/bedtools/bamtobed/main.nf
index fd782dec..e3d3ee21 100644
--- a/modules/nf-core/modules/bedtools/bamtobed/main.nf
+++ b/modules/nf-core/bedtools/bamtobed/main.nf
@@ -1,6 +1,6 @@
 process BEDTOOLS_BAMTOBED {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bedtools/bamtobed/meta.yml
rename to modules/nf-core/bedtools/bamtobed/meta.yml
diff --git a/modules/nf-core/bedtools/complement/main.nf b/modules/nf-core/bedtools/complement/main.nf
new file mode 100644
index 00000000..d539dbdb
--- /dev/null
+++ b/modules/nf-core/bedtools/complement/main.nf
@@ -0,0 +1,37 @@
+process BEDTOOLS_COMPLEMENT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
+        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+
+    input:
+    tuple val(meta), path(bed)
+    path  sizes
+
+    output:
+    tuple val(meta), path('*.bed'), emit: bed
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bedtools \\
+        complement \\
+        -i $bed \\
+        -g $sizes \\
+        $args \\
+        > ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bedtools/complement/meta.yml b/modules/nf-core/bedtools/complement/meta.yml
new file mode 100644
index 00000000..708a2161
--- /dev/null
+++ b/modules/nf-core/bedtools/complement/meta.yml
@@ -0,0 +1,43 @@
+name: bedtools_complement
+description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
+keywords:
+  - bed
+  - complement
+tools:
+  - bedtools:
+      description: |
+        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: Input BED file
+      pattern: "*.{bed}"
+  - sizes:
+      type: file
+      description: File which defines the chromosome lengths for a given genome
+      pattern: "*.{sizes}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
+      pattern: "*.{bed}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Emiller88"
+  - "@sruthipsuresh"
+  - "@drpatelh"
diff --git a/modules/nf-core/modules/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf
similarity index 98%
rename from modules/nf-core/modules/bedtools/genomecov/main.nf
rename to modules/nf-core/bedtools/genomecov/main.nf
index 4804d40a..05e359c9 100644
--- a/modules/nf-core/modules/bedtools/genomecov/main.nf
+++ b/modules/nf-core/bedtools/genomecov/main.nf
@@ -1,6 +1,6 @@
 process BEDTOOLS_GENOMECOV {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bedtools/genomecov/meta.yml
rename to modules/nf-core/bedtools/genomecov/meta.yml
diff --git a/modules/nf-core/modules/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf
similarity index 97%
rename from modules/nf-core/modules/bedtools/intersect/main.nf
rename to modules/nf-core/bedtools/intersect/main.nf
index 29f16adb..2dee297c 100644
--- a/modules/nf-core/modules/bedtools/intersect/main.nf
+++ b/modules/nf-core/bedtools/intersect/main.nf
@@ -1,6 +1,6 @@
 process BEDTOOLS_INTERSECT {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bedtools/intersect/meta.yml b/modules/nf-core/bedtools/intersect/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bedtools/intersect/meta.yml
rename to modules/nf-core/bedtools/intersect/meta.yml
diff --git a/modules/nf-core/modules/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf
similarity index 97%
rename from modules/nf-core/modules/bedtools/merge/main.nf
rename to modules/nf-core/bedtools/merge/main.nf
index 6d1daa03..ba7cd9eb 100644
--- a/modules/nf-core/modules/bedtools/merge/main.nf
+++ b/modules/nf-core/bedtools/merge/main.nf
@@ -1,6 +1,6 @@
 process BEDTOOLS_MERGE {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bedtools/merge/meta.yml
rename to modules/nf-core/bedtools/merge/meta.yml
diff --git a/modules/nf-core/modules/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
similarity index 100%
rename from modules/nf-core/modules/bowtie2/align/main.nf
rename to modules/nf-core/bowtie2/align/main.nf
diff --git a/modules/nf-core/modules/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
similarity index 98%
rename from modules/nf-core/modules/bowtie2/align/meta.yml
rename to modules/nf-core/bowtie2/align/meta.yml
index c99fa4e3..42ba0f96 100644
--- a/modules/nf-core/modules/bowtie2/align/meta.yml
+++ b/modules/nf-core/bowtie2/align/meta.yml
@@ -2,7 +2,9 @@ name: bowtie2_align
 description: Align reads to a reference genome using bowtie2
 keywords:
   - align
+  - map
   - fasta
+  - fastq
   - genome
   - reference
 tools:
diff --git a/modules/nf-core/modules/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
similarity index 100%
rename from modules/nf-core/modules/bowtie2/build/main.nf
rename to modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/nf-core/modules/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bowtie2/build/meta.yml
rename to modules/nf-core/bowtie2/build/meta.yml
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
similarity index 61%
rename from modules/nf-core/modules/cat/fastq/main.nf
rename to modules/nf-core/cat/fastq/main.nf
index b6854895..4fa365d3 100644
--- a/modules/nf-core/modules/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -1,6 +1,6 @@
 process CAT_FASTQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -20,9 +20,9 @@ process CAT_FASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
-        if (readList.size > 1) {
+        if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
 
@@ -33,7 +33,7 @@ process CAT_FASTQ {
             """
         }
     } else {
-        if (readList.size > 2) {
+        if (readList.size >= 2) {
             def read1 = []
             def read2 = []
             readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
@@ -48,4 +48,33 @@ process CAT_FASTQ {
             """
         }
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
+    if (meta.single_end) {
+        if (readList.size > 1) {
+            """
+            touch ${prefix}.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    } else {
+        if (readList.size > 2) {
+            """
+            touch ${prefix}_1.merged.fastq.gz
+            touch ${prefix}_2.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    }
+
 }
diff --git a/modules/nf-core/modules/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cat/fastq/meta.yml
rename to modules/nf-core/cat/fastq/meta.yml
diff --git a/modules/nf-core/modules/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
similarity index 51%
rename from modules/nf-core/modules/custom/getchromsizes/main.nf
rename to modules/nf-core/custom/getchromsizes/main.nf
index 0eabf3a4..8e1693d4 100644
--- a/modules/nf-core/modules/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -1,6 +1,6 @@
 process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -8,12 +8,13 @@ process CUSTOM_GETCHROMSIZES {
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path '*.sizes'      , emit: sizes
-    path '*.fai'        , emit: fai
-    path  "versions.yml", emit: versions
+    tuple val(meta), path ("*.sizes"), emit: sizes
+    tuple val(meta), path ("*.fai")  , emit: fai
+    tuple val(meta), path ("*.gzi")  , emit: gzi, optional: true
+    path  "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,7 +27,18 @@ process CUSTOM_GETCHROMSIZES {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        custom: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${fasta}.fai
+    touch ${fasta}.sizes
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml
similarity index 62%
rename from modules/nf-core/modules/custom/getchromsizes/meta.yml
rename to modules/nf-core/custom/getchromsizes/meta.yml
index ee6c2571..219ca1d8 100644
--- a/modules/nf-core/modules/custom/getchromsizes/meta.yml
+++ b/modules/nf-core/custom/getchromsizes/meta.yml
@@ -14,12 +14,22 @@ tools:
       licence: ["MIT"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: FASTA file
-      pattern: "*.{fasta}"
+      pattern: "*.{fa,fasta,fna,fas}"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - sizes:
       type: file
       description: File containing chromosome lengths
@@ -28,11 +38,16 @@ output:
       type: file
       description: FASTA index file
       pattern: "*.{fai}"
+  - gzi:
+      type: file
+      description: Optional gzip index file for compressed inputs
+      pattern: "*.gzi"
   - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
       pattern: "versions.yml"
 
 authors:
   - "@tamara-hodgetts"
   - "@chris-cheshire"
+  - "@muffato"
diff --git a/modules/nf-core/modules/deeptools/computematrix/main.nf b/modules/nf-core/deeptools/computematrix/main.nf
similarity index 100%
rename from modules/nf-core/modules/deeptools/computematrix/main.nf
rename to modules/nf-core/deeptools/computematrix/main.nf
diff --git a/modules/nf-core/modules/deeptools/computematrix/meta.yml b/modules/nf-core/deeptools/computematrix/meta.yml
similarity index 100%
rename from modules/nf-core/modules/deeptools/computematrix/meta.yml
rename to modules/nf-core/deeptools/computematrix/meta.yml
diff --git a/modules/nf-core/deeptools/plotfingerprint/main.nf b/modules/nf-core/deeptools/plotfingerprint/main.nf
new file mode 100644
index 00000000..83613be7
--- /dev/null
+++ b/modules/nf-core/deeptools/plotfingerprint/main.nf
@@ -0,0 +1,41 @@
+process DEEPTOOLS_PLOTFINGERPRINT {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' :
+        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(bams), path(bais)
+
+    output:
+    tuple val(meta), path("*.pdf")          , emit: pdf
+    tuple val(meta), path("*.raw.txt")      , emit: matrix
+    tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
+    path  "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extend   = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
+    """
+    plotFingerprint \\
+        $args \\
+        $extend \\
+        --bamfiles ${bams.join(' ')} \\
+        --plotFile ${prefix}.plotFingerprint.pdf \\
+        --outRawCounts ${prefix}.plotFingerprint.raw.txt \\
+        --outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
+        --numberOfProcessors $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(plotFingerprint --version | sed -e "s/plotFingerprint //g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/deeptools/plotfingerprint/meta.yml b/modules/nf-core/deeptools/plotfingerprint/meta.yml
new file mode 100644
index 00000000..07c25748
--- /dev/null
+++ b/modules/nf-core/deeptools/plotfingerprint/meta.yml
@@ -0,0 +1,61 @@
+name: deeptools_plotfingerprint
+description: plots cumulative reads coverages by BAM file
+keywords:
+  - plot
+  - fingerprint
+  - cumulative coverage
+  - bam
+tools:
+  - deeptools:
+      description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
+      homepage:
+      documentation: https://deeptools.readthedocs.io/en/develop/index.html
+      tool_dev_url: https://github.com/deeptools/deepTools
+      doi: "10.1093/nar/gku365"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: One or more BAM files
+      pattern: "*.{bam}"
+  - bais:
+      type: file
+      description: Corresponding BAM file indexes
+      pattern: "*.bam.bai"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - pdf:
+      type: file
+      description: |
+        Output figure containing resulting plot
+      pattern: "*.{plotFingerprint.pdf}"
+  - matrix:
+      type: file
+      description: |
+        Output file summarizing the read counts per bin
+      pattern: "*.{plotFingerprint.raw.txt}"
+  - metrics:
+      type: file
+      description: |
+        file containing BAM file quality metrics
+      pattern: "*.{qcmetrics.txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@emiller88"
+  - "@drpatelh"
+  - "@joseespinosa"
diff --git a/modules/nf-core/modules/deeptools/plotheatmap/main.nf b/modules/nf-core/deeptools/plotheatmap/main.nf
similarity index 100%
rename from modules/nf-core/modules/deeptools/plotheatmap/main.nf
rename to modules/nf-core/deeptools/plotheatmap/main.nf
diff --git a/modules/nf-core/modules/deeptools/plotheatmap/meta.yml b/modules/nf-core/deeptools/plotheatmap/meta.yml
similarity index 100%
rename from modules/nf-core/modules/deeptools/plotheatmap/meta.yml
rename to modules/nf-core/deeptools/plotheatmap/meta.yml
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
similarity index 100%
rename from modules/nf-core/modules/fastqc/main.nf
rename to modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fastqc/meta.yml
rename to modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
similarity index 75%
rename from modules/nf-core/modules/gunzip/main.nf
rename to modules/nf-core/gunzip/main.nf
index 61bf1afa..fa6ba26a 100644
--- a/modules/nf-core/modules/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -1,6 +1,6 @@
 process GUNZIP {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -31,4 +31,14 @@ process GUNZIP {
         gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    gunzip = archive.toString() - '.gz'
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/modules/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gunzip/meta.yml
rename to modules/nf-core/gunzip/meta.yml
diff --git a/modules/nf-core/modules/macs2/callpeak/main.nf b/modules/nf-core/macs2/callpeak/main.nf
similarity index 100%
rename from modules/nf-core/modules/macs2/callpeak/main.nf
rename to modules/nf-core/macs2/callpeak/main.nf
diff --git a/modules/nf-core/modules/macs2/callpeak/meta.yml b/modules/nf-core/macs2/callpeak/meta.yml
similarity index 100%
rename from modules/nf-core/modules/macs2/callpeak/meta.yml
rename to modules/nf-core/macs2/callpeak/meta.yml
diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
similarity index 92%
rename from modules/nf-core/modules/picard/markduplicates/main.nf
rename to modules/nf-core/picard/markduplicates/main.nf
index 87f913d4..4e559fea 100644
--- a/modules/nf-core/modules/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/modules/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml
similarity index 100%
rename from modules/nf-core/modules/picard/markduplicates/meta.yml
rename to modules/nf-core/picard/markduplicates/meta.yml
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
new file mode 100644
index 00000000..ef940db2
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -0,0 +1,44 @@
+process SAMTOOLS_FAIDX {
+    tag "$fasta"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path ("*.fai"), emit: fai
+    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools \\
+        faidx \\
+        $args \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${fasta}.fai
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
new file mode 100644
index 00000000..fe2fe9a1
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -0,0 +1,47 @@
+name: samtools_faidx
+description: Index FASTA file
+keywords:
+  - index
+  - fasta
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa,fasta}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fai:
+      type: file
+      description: FASTA index file
+      pattern: "*.{fai}"
+  - gzi:
+      type: file
+      description: Optional gzip index file for compressed inputs
+      pattern: "*.gzi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@ewels"
+  - "@phue"
diff --git a/modules/nf-core/modules/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
similarity index 86%
rename from modules/nf-core/modules/samtools/flagstat/main.nf
rename to modules/nf-core/samtools/flagstat/main.nf
index b87b2108..c3152aca 100644
--- a/modules/nf-core/modules/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -19,12 +19,13 @@ process SAMTOOLS_FLAGSTAT {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     samtools \\
         flagstat \\
-        --threads ${task.cpus-1} \\
+        --threads ${task.cpus} \\
         $bam \\
-        > ${bam}.flagstat
+        > ${prefix}.flagstat
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/flagstat/meta.yml
rename to modules/nf-core/samtools/flagstat/meta.yml
diff --git a/modules/nf-core/modules/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
similarity index 88%
rename from modules/nf-core/modules/samtools/idxstats/main.nf
rename to modules/nf-core/samtools/idxstats/main.nf
index a49ff35f..87618e5f 100644
--- a/modules/nf-core/modules/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -19,11 +19,14 @@ process SAMTOOLS_IDXSTATS {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
     samtools \\
         idxstats \\
+        --threads ${task.cpus-1} \\
         $bam \\
-        > ${bam}.idxstats
+        > ${prefix}.idxstats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/idxstats/meta.yml
rename to modules/nf-core/samtools/idxstats/meta.yml
diff --git a/modules/nf-core/modules/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/index/main.nf
rename to modules/nf-core/samtools/index/main.nf
diff --git a/modules/nf-core/modules/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/index/meta.yml
rename to modules/nf-core/samtools/index/meta.yml
diff --git a/modules/nf-core/modules/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
similarity index 95%
rename from modules/nf-core/modules/samtools/sort/main.nf
rename to modules/nf-core/samtools/sort/main.nf
index b4fc1cbe..ab7f1cca 100644
--- a/modules/nf-core/modules/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -12,6 +12,7 @@ process SAMTOOLS_SORT {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.csi"), emit: csi, optional: true
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/nf-core/modules/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
similarity index 92%
rename from modules/nf-core/modules/samtools/sort/meta.yml
rename to modules/nf-core/samtools/sort/meta.yml
index a820c55a..09289751 100644
--- a/modules/nf-core/modules/samtools/sort/meta.yml
+++ b/modules/nf-core/samtools/sort/meta.yml
@@ -39,6 +39,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - csi:
+      type: file
+      description: BAM index file (optional)
+      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@ewels"
diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
similarity index 88%
rename from modules/nf-core/modules/samtools/stats/main.nf
rename to modules/nf-core/samtools/stats/main.nf
index bbdc3240..9b0c3867 100644
--- a/modules/nf-core/modules/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_STATS {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -20,14 +20,15 @@ process SAMTOOLS_STATS {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
     """
     samtools \\
         stats \\
-        --threads ${task.cpus-1} \\
+        --threads ${task.cpus} \\
         ${reference} \\
         ${input} \\
-        > ${input}.stats
+        > ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +39,7 @@ process SAMTOOLS_STATS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${input}.stats
+    touch ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/stats/meta.yml
rename to modules/nf-core/samtools/stats/meta.yml
diff --git a/modules/nf-core/modules/seacr/callpeak/main.nf b/modules/nf-core/seacr/callpeak/main.nf
similarity index 83%
rename from modules/nf-core/modules/seacr/callpeak/main.nf
rename to modules/nf-core/seacr/callpeak/main.nf
index 340c0eef..f0311f2f 100644
--- a/modules/nf-core/modules/seacr/callpeak/main.nf
+++ b/modules/nf-core/seacr/callpeak/main.nf
@@ -1,9 +1,8 @@
-def VERSION = '1.3' // Version information not provided by tool on CLI
-
 process SEACR_CALLPEAK {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' :
@@ -24,6 +23,7 @@ process SEACR_CALLPEAK {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
+    def VERSION = '1.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     SEACR_1.3.sh \\
         $bedgraph \\
diff --git a/modules/nf-core/modules/seacr/callpeak/meta.yml b/modules/nf-core/seacr/callpeak/meta.yml
similarity index 100%
rename from modules/nf-core/modules/seacr/callpeak/meta.yml
rename to modules/nf-core/seacr/callpeak/meta.yml
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
new file mode 100644
index 00000000..0d05984a
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -0,0 +1,45 @@
+process TABIX_BGZIPTABIX {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
+        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
+    path  "versions.yml" ,                        emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bgzip  --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
+    tabix $args2 ${prefix}.${input.getExtension()}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gz
+    touch ${prefix}.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
new file mode 100644
index 00000000..49c03289
--- /dev/null
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -0,0 +1,45 @@
+name: tabix_bgziptabix
+description: bgzip a sorted tab-delimited genome file and then create tabix index
+keywords:
+  - bgzip
+  - compress
+  - index
+  - tabix
+  - vcf
+tools:
+  - tabix:
+      description: Generic indexer for TAB-delimited genome position files.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: https://www.htslib.org/doc/tabix.1.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tab:
+      type: file
+      description: TAB-delimited genome position file
+      pattern: "*.{bed,gff,sam,vcf}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gz:
+      type: file
+      description: Output compressed file
+      pattern: "*.{gz}"
+  - tbi:
+      type: file
+      description: tabix index file
+      pattern: "*.{gz.tbi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@maxulysse"
diff --git a/modules/nf-core/modules/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf
old mode 100644
new mode 100755
similarity index 77%
rename from modules/nf-core/modules/ucsc/bedclip/main.nf
rename to modules/nf-core/ucsc/bedclip/main.nf
index 969a8f73..42dd08bb
--- a/modules/nf-core/modules/ucsc/bedclip/main.nf
+++ b/modules/nf-core/ucsc/bedclip/main.nf
@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BEDCLIP {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' :
@@ -23,6 +22,7 @@ process UCSC_BEDCLIP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedClip \\
         $bedgraph \\
diff --git a/modules/nf-core/modules/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml
old mode 100644
new mode 100755
similarity index 100%
rename from modules/nf-core/modules/ucsc/bedclip/meta.yml
rename to modules/nf-core/ucsc/bedclip/meta.yml
diff --git a/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
similarity index 76%
rename from modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
rename to modules/nf-core/ucsc/bedgraphtobigwig/main.nf
index ef0ca088..a2979e04 100644
--- a/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BEDGRAPHTOBIGWIG {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' :
@@ -23,6 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedGraphToBigWig \\
         $bedgraph \\
diff --git a/modules/nf-core/modules/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
old mode 100644
new mode 100755
similarity index 100%
rename from modules/nf-core/modules/ucsc/bedgraphtobigwig/meta.yml
rename to modules/nf-core/ucsc/bedgraphtobigwig/meta.yml
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/untar/main.nf
similarity index 67%
rename from modules/nf-core/modules/untar/main.nf
rename to modules/nf-core/untar/main.nf
index 29ab10a5..71eea7b2 100644
--- a/modules/nf-core/modules/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -1,6 +1,6 @@
 process UNTAR {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -25,12 +25,23 @@ process UNTAR {
     """
     mkdir output
 
-    tar \\
-        -C output --strip-components 1 \\
-        -xzvf \\
-        $args \\
-        $archive \\
-        $args2
+    ## Ensures --strip-components only applied when top level of tar contents is a directory
+    ## If just files or multiple directories, place all in output
+    if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+        tar \\
+            -C output --strip-components 1 \\
+            -xzvf \\
+            $args \\
+            $archive \\
+            $args2
+    else
+        tar \\
+            -C output \\
+            -xzvf \\
+            $args \\
+            $archive \\
+            $args2
+    fi
 
     mv output ${untar}
 
diff --git a/modules/nf-core/modules/untar/meta.yml b/modules/nf-core/untar/meta.yml
similarity index 85%
rename from modules/nf-core/modules/untar/meta.yml
rename to modules/nf-core/untar/meta.yml
index d426919b..ea7a3f38 100644
--- a/modules/nf-core/modules/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -26,9 +26,9 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - untar:
-      type: file
-      description:
-      pattern: "*.*"
+      type: directory
+      description: Directory containing contents of archive
+      pattern: "*/"
   - versions:
       type: file
       description: File containing software versions
@@ -36,3 +36,5 @@ output:
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@matthdsm"
+  - "@jfy133"
diff --git a/nextflow.config b/nextflow.config
index 927e0fe7..99e2a700 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,7 @@ params {
     genome                     = null
     spikein_genome             = "K12-MG1655"
     gene_bed                   = null
+    blacklist                  = null
     save_reference             = false
     only_genome                = false
 
@@ -49,7 +50,7 @@ params {
     save_align_intermed        = false
 
     // Filtering
-    minimum_alignment_q_score  = 0
+    minimum_alignment_q_score  = 20
 
     // Deduplication
     skip_removeduplicates      = false
@@ -58,34 +59,49 @@ params {
 
     // Read Normalisation
     normalisation_mode         = "Spikein"
-    normalisation_binsize      = 1
+    normalisation_binsize      = 50
     normalisation_c            = 10000
-    igg_scale_factor           = 1
+    igg_scale_factor           = 0.5
 
     // Peak Caller default param
     peakcaller                 = 'seacr'
 
-    // SEACR Peak Calling
+    // Peak Calling
     use_control                = true
-    peak_threshold             = 0.05
     only_peak_calling          = false
-
-    // MACS2 Peak Calling
+    extend_fragments           = true
+    seacr_norm                 = 'non'
+    seacr_stringent            = 'stringent'
+    seacr_peak_threshold       = 0.05
     macs2_pvalue               = 0.05
-    macs_gsize                = 2.7e9
-    run_narrow_peak            = false
+    macs_gsize                 = 2.7e9
+    macs2_narrow_peak          = true
+    macs2_broad_cutoff         = 0.1
 
     // Consensus Peaks
     consensus_peak_mode        = 'group'
     replicate_threshold        = 1
-    skip_upset_plots           = false
 
     // Reporting and Visualisation
     skip_reporting             = false
     skip_igv                   = false
     skip_heatmaps              = false
+    skip_dt_qc                 = false
+    skip_peak_qc               = false
+    skip_preseq                = false
     skip_multiqc               = false
-    skip_frip                  = false
+    igv_show_gene_names        = true
+    min_frip_overlap           = 0.20
+    min_peak_overlap           = 0.20
+
+    // Deeptools options
+    dt_heatmap_gene_bodylen    = 5000
+    dt_heatmap_gene_beforelen  = 3000
+    dt_heatmap_gene_afterlen   = 3000
+    dt_heatmap_peak_beforelen  = 3000
+    dt_heatmap_peak_afterlen   = 3000
+    dt_qc_bam_binsize          = 500
+    fragment_size              = 100 // PARAM NOT USED
 
     // Boilerplate options
     outdir                     = "./results"
@@ -97,15 +113,17 @@ params {
     max_multiqc_email_size     = "25.MB"
     plaintext_email            = false
     monochrome_logs            = false
+    hook_url                   = null
     help                       = false
     igenomes_base              = "s3://ngi-igenomes/igenomes/"
     tracedir                   = "${params.outdir}/pipeline_info"
     igenomes_ignore            = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes,callers,dedup_control_only,run_igv,run_peak_plotting,run_multiqc,run_deep_tools,run_reporting,run_consensus_all,run_peak_calling,run_remove_dups,run_mark_dups,run_q_filter,run_alignment,run_trim_galore_fastqc,run_cat_fastq,run_input_check,run_genome_prep'
+    schema_ignore_params       = 'genomes,callers,dedup_control_only,fragment_size,run_igv,run_multiqc,run_reporting,run_consensus_all,run_peak_calling,run_remove_dups,run_mark_dups,run_read_filter,run_alignment,run_trim_galore_fastqc,run_cat_fastq,run_input_check,run_genome_prep,run_peak_qc,run_deeptools_qc,run_deeptools_heatmaps,run_preseq'
     enable_conda               = false
 
+
     // Config options
     custom_config_version      = "master"
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -114,6 +132,7 @@ params {
     config_profile_contact     = null
     config_profile_url         = null
 
+
     // Max resource options
     max_memory                 = "128.GB"
     max_cpus                   = 16
@@ -151,6 +170,15 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
+    mamba {
+        params.enable_conda    = true
+        conda.useMamba         = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
     docker {
         docker.enabled         = true
         // Avoid this error:
@@ -205,6 +233,7 @@ profiles {
     test_full_small_local_zip { includeConfig "conf/test_full_small_local_zip.config" } // Runs a full experimental configuration but with a small dataset but that targets local, already downloaded compressed input files
 }
 
+
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
     includeConfig 'conf/igenomes.config'
@@ -212,6 +241,7 @@ if (!params.igenomes_ignore) {
     params.genomes = [:]
 }
 
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -252,7 +282,7 @@ manifest {
     description     = 'Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '2.0.0'
+    version = '3.0.0'
 }
 
 // Load flowswitch.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 02133b0c..6f8649b1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -202,30 +202,34 @@
                     "fa_icon": "fas fa-random",
                     "description": "Skips reporting"
                 },
+                "skip_preseq": {
+                    "type": "boolean",
+                    "description": "Skips preseq reporting"
+                },
                 "skip_igv": {
                     "type": "boolean",
                     "fa_icon": "fas fa-random",
                     "description": "Skips igv session generation"
                 },
+                "skip_dt_qc": {
+                    "type": "boolean",
+                    "description": "Skips deeptools QC repoting",
+                    "fa_icon": "fas fa-random"
+                },
                 "skip_heatmaps": {
                     "type": "boolean",
                     "fa_icon": "fas fa-random",
                     "description": "Skips deeptools heatmap generation"
                 },
-                "skip_multiqc": {
+                "skip_peak_qc": {
                     "type": "boolean",
-                    "fa_icon": "fas fa-random",
-                    "description": "Skips multiqc"
+                    "description": "Skips peak QC reporting",
+                    "fa_icon": "fas fa-random"
                 },
-                "skip_upset_plots": {
+                "skip_multiqc": {
                     "type": "boolean",
                     "fa_icon": "fas fa-random",
-                    "description": "Skip upset plot calculation"
-                },
-                "skip_frip": {
-                    "type": "boolean",
-                    "description": "Skip fragments in peaks calculation",
-                    "fa_icon": "fas fa-random"
+                    "description": "Skips multiqc"
                 }
             },
             "fa_icon": "fas fa-exchange-alt"
@@ -314,12 +318,6 @@
                     "description": "If normsalisation option is one of  \"RPKM\", \"CPM\", \"BPM\" - then the binsize that the reads count is calculated on is used.",
                     "fa_icon": "fas fa-arrows-alt-h"
                 },
-                "peak_threshold": {
-                    "type": "number",
-                    "default": 0.05,
-                    "fa_icon": "fas fa-grip-lines",
-                    "description": "Threshold for peak calling when no IgG is present"
-                },
                 "peakcaller": {
                     "type": "string",
                     "default": "seacr",
@@ -332,12 +330,38 @@
                     "fa_icon": "fas fa-align-justify",
                     "description": "Specifies whether to use a control to normalise peak calls against (e.g. IgG)"
                 },
+                "extend_fragments": {
+                    "type": "boolean",
+                    "default": true,
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks"
+                },
                 "igg_scale_factor": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 0.5,
                     "fa_icon": "fas fa-align-justify",
                     "description": "Specifies whether the background control is scaled prior to being used to normalise peaks."
                 },
+                "seacr_peak_threshold": {
+                    "type": "number",
+                    "default": 0.05,
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "SEACR p-value threshold for peaks"
+                },
+                "seacr_norm": {
+                    "type": "string",
+                    "default": "non",
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "SEACR normalization. ",
+                    "enum": ["non", "norm"]
+                },
+                "seacr_stringent": {
+                    "type": "string",
+                    "default": "stringent",
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "SEACR stringency.",
+                    "enum": ["stringent", "relaxed"]
+                },
                 "macs2_pvalue": {
                     "type": "number",
                     "default": 0.05,
@@ -350,10 +374,17 @@
                     "fa_icon": "fas fa-align-justify",
                     "description": "parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize will default to GRCh38."
                 },
-                "run_narrow_peak": {
+                "macs2_narrow_peak": {
                     "type": "boolean",
+                    "default": true,
                     "fa_icon": "fas fa-align-justify",
-                    "description": "Specifies whether to run macs2 in narrow peak mode"
+                    "description": "Determines whether MACS2 broad or narrow peak mode is used for the peak caller"
+                },
+                "macs2_broad_cutoff": {
+                    "type": "number",
+                    "default": 0.1,
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "MACS2 broad cutoff parameter"
                 },
                 "consensus_peak_mode": {
                     "type": "string",
@@ -367,10 +398,73 @@
                     "default": 1.0,
                     "fa_icon": "fas fa-align-justify",
                     "description": "Minimum number of overlapping replicates needed for a consensus peak"
+                },
+                "igv_show_gene_names": {
+                    "type": "boolean",
+                    "default": true,
+                    "fa_icon": "fas fa-align-justify",
+                    "description": "Show gene names instead of symbols in IGV browser sessions"
                 }
             },
             "fa_icon": "fas fa-cog"
         },
+        "reporting_options": {
+            "title": "Reporting Options",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "fa_icon": "fas fa-atlas",
+            "properties": {
+                "dt_qc_bam_binsize": {
+                    "type": "integer",
+                    "default": 500,
+                    "description": "Deeptools multiBamSummary bam bin size",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "dt_heatmap_gene_beforelen": {
+                    "type": "integer",
+                    "default": 3000,
+                    "description": "Deeptools heatmap gene plot before length (bases)",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "dt_heatmap_gene_bodylen": {
+                    "type": "integer",
+                    "default": 5000,
+                    "description": "Deeptools heatmap gene plot body length (bases)",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "dt_heatmap_gene_afterlen": {
+                    "type": "integer",
+                    "default": 3000,
+                    "description": "Deeptools heatmap gene plot after length (bases)",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "dt_heatmap_peak_beforelen": {
+                    "type": "integer",
+                    "default": 3000,
+                    "description": "Deeptools heatmap peak plot before length (bases)",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "dt_heatmap_peak_afterlen": {
+                    "type": "integer",
+                    "default": 3000,
+                    "description": "Deeptools heatmap peak plot after length (bases)",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "min_frip_overlap": {
+                    "type": "number",
+                    "default": 0.2,
+                    "description": "Minimum fragment overlap for FriP score",
+                    "fa_icon": "fas fa-align-justify"
+                },
+                "min_peak_overlap": {
+                    "type": "number",
+                    "default": 0.2,
+                    "description": "Minimum peak overlap for peak reproducibility plot",
+                    "fa_icon": "fas fa-align-justify"
+                }
+            }
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -504,6 +598,13 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
+                "hook_url": {
+                    "type": "string",
+                    "description": "Incoming hook URL for messaging service",
+                    "fa_icon": "fas fa-people-group",
+                    "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.",
+                    "hidden": true
+                },
                 "multiqc_config": {
                     "type": "string",
                     "description": "Custom config file to supply to MultiQC.",
@@ -556,6 +657,9 @@
         {
             "$ref": "#/definitions/pipeline_options"
         },
+        {
+            "$ref": "#/definitions/reporting_options"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..0d62beb6
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3
diff --git a/subworkflows/local/align_bowtie2.nf b/subworkflows/local/align_bowtie2.nf
index 0a210c89..97ac616e 100644
--- a/subworkflows/local/align_bowtie2.nf
+++ b/subworkflows/local/align_bowtie2.nf
@@ -2,8 +2,8 @@
  * Alignment with BOWTIE2
  */
 
-include { BOWTIE2_ALIGN                                  } from '../../modules/nf-core/modules/bowtie2/align/main'
-include { BOWTIE2_ALIGN as BOWTIE2_SPIKEIN_ALIGN         } from '../../modules/nf-core/modules/bowtie2/align/main'
+include { BOWTIE2_ALIGN                                  } from '../../modules/nf-core/bowtie2/align/main'
+include { BOWTIE2_ALIGN as BOWTIE2_SPIKEIN_ALIGN         } from '../../modules/nf-core/bowtie2/align/main'
 include { BAM_SORT_SAMTOOLS                              } from '../nf-core/bam_sort_samtools'
 include { BAM_SORT_SAMTOOLS as BAM_SORT_SAMTOOLS_SPIKEIN } from '../nf-core/bam_sort_samtools'
 
diff --git a/subworkflows/local/annotate_meta_awk.nf b/subworkflows/local/annotate_meta_awk.nf
deleted file mode 100644
index e0206c37..00000000
--- a/subworkflows/local/annotate_meta_awk.nf
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Annotate the pipeline meta data with the columns from a csv file
- * generated from processing a report text file with an awk script
- */
-
-include { AWK_SCRIPT } from '../../modules/local/linux/awk_script'
-include { AWK }        from '../../modules/local/linux/awk'
-
-workflow ANNOTATE_META_AWK {
-    take:
-    passthrough
-    report
-    script
-    meta_prefix // string
-    meta_suffix // string
-    script_mode // bool
-
-    main:
-    ch_versions = Channel.empty()
-
-    // Strip out the sample id from the meta in the passthrough
-    ch_paths = passthrough.map { row -> [row[0].id, row[0], row[1..-1]].flatten() }
-
-    ch_annotated_meta = Channel.empty()
-    // Can run awk in script mode with a file from assets or with a setup of command line args
-    if(script_mode) {
-        AWK_SCRIPT ( report, script )
-        ch_versions = ch_versions.mix(AWK_SCRIPT.out.versions)
-
-        AWK_SCRIPT.out.file
-            .splitCsv(header:true)
-            .map { row ->
-                new_meta = [:]
-                row[1].each{ k, v -> new_meta.put(meta_prefix + k + meta_suffix, v) }
-                [row[0].id, new_meta]
-            }
-            .join ( ch_paths )
-            .map { row -> [ row[2] << row[1], row[3..-1] ] }
-            .set { ch_annotated_meta }
-    }
-    else {
-        AWK ( report )
-        ch_versions = ch_versions.mix(AWK.out.versions)
-
-        AWK.out.file
-            .splitCsv(header:true)
-            .map { row ->
-                new_meta = [:]
-                row[1].each{ k, v -> new_meta.put(meta_prefix + k + meta_suffix, v) }
-                [row[0].id, new_meta]
-            }
-            .join ( ch_paths )
-            .map { row -> [ row[2] << row[1], row[3..-1] ] }
-            .set { ch_annotated_meta }
-    }
-
-    emit:
-    output     = ch_annotated_meta // channel: [ val(annotated_meta), [ passthrough ] ]
-    versions   = ch_versions       // channel: [ versions.yml ]
-}
diff --git a/subworkflows/local/annotate_meta_csv.nf b/subworkflows/local/annotate_meta_csv.nf
deleted file mode 100644
index e7423351..00000000
--- a/subworkflows/local/annotate_meta_csv.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * Annotate the pipeline meta data with a csv file
- */
-
-workflow ANNOTATE_META_CSV {
-    take:
-    passthrough // channel
-    reports     // file
-    meta_suffix // string
-    meta_prefix // string
-
-    main:
-
-    main:
-    // Strip out the sample id from the meta in the passthrough
-    ch_paths = passthrough.map { row -> [row[0].id, row[0], row[1..-1]].flatten() }
-
-    reports.splitCsv(header:true)
-        .map { row ->
-            new_meta = [:]
-            row[1].each{ k, v -> new_meta.put(meta_prefix + k + meta_suffix, v) }
-            [row[0].id, new_meta]
-        }
-        .join ( ch_paths )
-        .map { row -> [ row[2] << row[1], row[3..-1] ] }
-        .set { ch_annotated_meta }
-
-    emit:
-    output = ch_annotated_meta // channel: [ val(annotated_meta), [ passthrough ] ]
-}
diff --git a/subworkflows/local/calculate_fragments.nf b/subworkflows/local/calculate_fragments.nf
deleted file mode 100644
index 171358b7..00000000
--- a/subworkflows/local/calculate_fragments.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Calculate bed fragments from bam file
- */
-
-include { SAMTOOLS_VIEW      } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_SORT      } from '../../modules/nf-core/modules/samtools/sort/main'
-include { BEDTOOLS_BAMTOBED  } from '../../modules/nf-core/modules/bedtools/bamtobed/main'
-include { AWK                } from '../../modules/local/linux/awk'
-include { CUT                } from '../../modules/local/linux/cut'
-
-workflow CALCULATE_FRAGMENTS {
-    take:
-    bam // channel: [ val(meta), [ bam ] ]
-
-    main:
-    ch_versions = Channel.empty()
-
-    /*
-     * Filter BAM file
-     */
-    SAMTOOLS_VIEW ( bam.map{ row -> [ row[0], row[1], [] ] }, [] )
-    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions)
-
-    /*
-    * Sort BAM file
-    */
-    SAMTOOLS_SORT ( SAMTOOLS_VIEW.out.bam )
-    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
-
-    // Convert to bed file
-    BEDTOOLS_BAMTOBED ( SAMTOOLS_SORT.out.bam  )
-    ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions)
-
-    // Keep the read pairs that are on the same chromosome and fragment length less than 1000bp.
-    AWK ( BEDTOOLS_BAMTOBED.out.bed  )
-    ch_versions = ch_versions.mix(AWK.out.versions)
-
-    // Only extract the fragment related columns
-    CUT ( AWK.out.file )
-
-    emit:
-    bed              = CUT.out.file                   // channel: [ val(meta), [ bed ] ]
-    bam              = SAMTOOLS_SORT.out.bam          // channel: [ val(meta), [ bam ] ]
-    versions         = ch_versions                    // channel: [ versions.yml ]
-}
diff --git a/subworkflows/local/consensus_peaks.nf b/subworkflows/local/consensus_peaks.nf
index 4c848f88..630c7b84 100644
--- a/subworkflows/local/consensus_peaks.nf
+++ b/subworkflows/local/consensus_peaks.nf
@@ -1,17 +1,14 @@
 /*
- * Create group consensus peaks
+ * Create group-level consensus peaks
  */
 
 include { SORT                 } from '../../modules/local/linux/sort'
-include { BEDTOOLS_MERGE       } from '../../modules/nf-core/modules/bedtools/merge/main'
+include { BEDTOOLS_MERGE       } from '../../modules/nf-core/bedtools/merge/main'
 include { AWK                  } from '../../modules/local/linux/awk'
-include { PLOT_CONSENSUS_PEAKS } from '../../modules/local/modules/plot_consensus_peaks/main'
 
 workflow CONSENSUS_PEAKS {
-
     take:
-    bed       //  channel: [ val(meta), [ bed ], count]
-    skip_plot // boolean: true/false
+    bed //  channel: [ val(meta), [ bed ], count]
 
     main:
     ch_versions = Channel.empty()
@@ -28,14 +25,8 @@ workflow CONSENSUS_PEAKS {
     AWK ( BEDTOOLS_MERGE.out.bed )
     ch_versions = ch_versions.mix(AWK.out.versions)
 
-    // Plot consensus peak sets
-    if(!skip_plot) {
-        PLOT_CONSENSUS_PEAKS ( BEDTOOLS_MERGE.out.bed.collect{it[1]} )
-        ch_versions = ch_versions.mix(PLOT_CONSENSUS_PEAKS.out.versions)
-    }
-
     emit:
-    bed               = BEDTOOLS_MERGE.out.bed        // channel: [ val(meta), [ bed ] ]
-    filtered_bed      = AWK.out.file                  // channel: [ val(meta), [ bed ] ]
-    versions          = ch_versions                   // channel: [ versions.yml       ]
+    merged_bed   = BEDTOOLS_MERGE.out.bed  // channel: [ val(meta), [ bed ] ]
+    filtered_bed = AWK.out.file            // channel: [ val(meta), [ bed ] ]
+    versions     = ch_versions             // channel: [ versions.yml       ]
 }
diff --git a/subworkflows/local/extract_fragments.nf b/subworkflows/local/extract_fragments.nf
new file mode 100644
index 00000000..11c4157d
--- /dev/null
+++ b/subworkflows/local/extract_fragments.nf
@@ -0,0 +1,50 @@
+/*
+ * Extract fragments from a BAM file into a bedfile format
+*/
+
+include { SAMTOOLS_SORT      } from "../../modules/nf-core/samtools/sort/main.nf"
+include { BEDTOOLS_BAMTOBED  } from "../../modules/nf-core/bedtools/bamtobed/main.nf"
+include { AWK                } from '../../modules/local/linux/awk'
+include { CUT                } from '../../modules/local/linux/cut'
+
+workflow EXTRACT_FRAGMENTS {
+    take:
+    bam // channel: [ val(meta), [ bam ] ]
+    main:
+    ch_versions = Channel.empty()
+
+    /*
+    * MODULE: Sort reads by name for bamtobed
+    */
+    SAMTOOLS_SORT (
+        bam
+    )
+
+    /*
+    * MODULE: Convert BAM file to paired-end bed format
+    */
+    BEDTOOLS_BAMTOBED(
+        SAMTOOLS_SORT.out.bam
+    )
+    ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions)
+    // BEDTOOLS_BAMTOBED.out.bed | view
+
+    /*
+    * MODULE: Keep the read pairs that are on the same chromosome and fragment length less than 1000bp.
+    */
+    AWK (
+        BEDTOOLS_BAMTOBED.out.bed  
+    )
+    ch_versions = ch_versions.mix(AWK.out.versions)
+
+    /*
+    * MODULE: Only extract the fragment related columns
+    */
+    CUT (
+        AWK.out.file
+    )
+
+    emit:
+    bed      = CUT.out.file // channel: [ val(meta), [ bed ] ]
+    versions = ch_versions  // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/extract_metadata_awk.nf b/subworkflows/local/extract_metadata_awk.nf
new file mode 100644
index 00000000..29adde36
--- /dev/null
+++ b/subworkflows/local/extract_metadata_awk.nf
@@ -0,0 +1,33 @@
+/*
+ * Generate table-based metadata from a summary report using AWK 
+ */
+
+include { AWK_SCRIPT } from '../../modules/local/linux/awk_script'
+include { AWK }        from '../../modules/local/linux/awk'
+
+workflow EXTRACT_METADATA_AWK {
+    take:
+    report
+    script
+    script_mode // bool
+
+    main:
+    ch_versions = Channel.empty()
+    ch_metadata = Channel.empty()
+
+    // Can run awk in script mode with a file from assets or with a setup of command line args
+    if(script_mode) {
+        AWK_SCRIPT ( report, script )
+        ch_metadata = AWK_SCRIPT.out.file
+        ch_versions = ch_versions.mix(AWK_SCRIPT.out.versions)
+    }
+    else {
+        AWK ( report )
+        ch_metadata = AWK.out.file
+        ch_versions = ch_versions.mix(AWK.out.versions)
+    }
+
+    emit:
+    metadata   = ch_metadata // channel: [ val(meta), [ metdatafile ] ]
+    versions   = ch_versions // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/fastqc_trimgalore.nf b/subworkflows/local/fastqc_trimgalore.nf
index 077d0649..e130465f 100644
--- a/subworkflows/local/fastqc_trimgalore.nf
+++ b/subworkflows/local/fastqc_trimgalore.nf
@@ -2,8 +2,8 @@
  * Read QC, read trimming and post trim QC
  */
 
-include { FASTQC     } from '../../modules/nf-core/modules/fastqc/main'
-include { TRIMGALORE } from '../../modules/local/modules/trimgalore/main'
+include { FASTQC     } from '../../modules/nf-core/fastqc/main'
+include { TRIMGALORE } from '../../modules/local/for_patch/trimgalore/main'
 
 workflow FASTQC_TRIMGALORE {
     take:
@@ -35,7 +35,6 @@ workflow FASTQC_TRIMGALORE {
         trim_zip        = TRIMGALORE.out.zip
         trim_log        = TRIMGALORE.out.log
         ch_versions     = ch_versions.mix(TRIMGALORE.out.versions)
-
     }
 
     emit:
diff --git a/subworkflows/local/peak_qc.nf b/subworkflows/local/peak_qc.nf
new file mode 100644
index 00000000..69b86047
--- /dev/null
+++ b/subworkflows/local/peak_qc.nf
@@ -0,0 +1,159 @@
+/*
+ * Calculate Peak-based metrics and QC
+*/
+
+include { PEAK_FRIP                            } from "../../modules/local/peak_frip"
+include { PEAK_COUNTS as PRIMARY_PEAK_COUNTS   } from "../../modules/local/peak_counts"
+include { PEAK_COUNTS as CONSENSUS_PEAK_COUNTS } from "../../modules/local/peak_counts"
+include { CUT as CUT_CALC_REPROD               } from "../../modules/local/linux/cut"
+include { BEDTOOLS_INTERSECT                   } from "../../modules/nf-core/bedtools/intersect/main.nf"
+include { CALCULATE_PEAK_REPROD                } from "../../modules/local/python/peak_reprod"
+include { PLOT_CONSENSUS_PEAKS                 } from '../../modules/local/python/plot_consensus_peaks'
+
+workflow PEAK_QC {
+    take:
+    peaks                               // channel: [ val(meta), [ bed ] ]
+    peaks_with_ids                      // channel: [ val(meta), [ bed ] ]
+    consensus_peaks                     // channel: [ val(meta), [ bed ] ]
+    consensus_peaks_unfiltered          // channel: [ val(meta), [ bed ] ]
+    fragments_bed                       // channel: [ val(meta), [ bed ] ]
+    flagstat                            // channel: [ val(meta), [ flagstat ] ]
+    min_frip_overlap                    // val
+    frip_score_header_multiqc           // file
+    peak_count_header_multiqc           // file
+    peak_count_consensus_header_multiqc // file
+    peak_reprod_header_multiqc          // file
+
+    main:
+    ch_versions = Channel.empty()
+
+    /*
+    * CHANNEL: Combine channel together for frip calculation
+    */
+    peaks
+    .map { row -> [row[0].id, row ].flatten()}
+    .join ( fragments_bed.map { row -> [row[0].id, row ].flatten()} )
+    .join ( flagstat.map { row -> [row[0].id, row ].flatten()} )
+    .map { row -> [ row[1], row[2], row[4], row[6] ]}
+    .set { ch_frip }
+    //ch_frip | view 
+
+    /*
+    * MODULE: Calculate frip scores for primary peaks
+    */
+    PEAK_FRIP(
+        ch_frip,
+        frip_score_header_multiqc,
+        min_frip_overlap
+    )
+    ch_versions = ch_versions.mix(PEAK_FRIP.out.versions)
+    // PEAK_FRIP.out.frip_mqc | view 
+
+    /*
+    * MODULE: Calculate peak counts for primary peaks
+    */
+    PRIMARY_PEAK_COUNTS(
+        peaks,
+        peak_count_header_multiqc
+    )
+    ch_versions = ch_versions.mix(PRIMARY_PEAK_COUNTS.out.versions)
+    // PRIMARY_PEAK_COUNTS.out.count_mqc | view
+
+    /*
+    * MODULE: Calculate peak counts for consensus peaks
+    */
+    CONSENSUS_PEAK_COUNTS(
+        consensus_peaks,
+        peak_count_consensus_header_multiqc
+    )
+    ch_versions = ch_versions.mix(CONSENSUS_PEAK_COUNTS.out.versions)
+    // CONSENSUS_PEAK_COUNTS.out.count_mqc | view
+
+    /*
+    * MODULE: Trim unwanted columns for downstream reporting
+    */
+    CUT_CALC_REPROD (
+        peaks_with_ids
+    )
+    ch_versions = ch_versions.mix(CUT_CALC_REPROD.out.versions)
+
+    /*
+    * CHANNEL: Group samples based on group and filter for groups that have more than one file
+    */
+    CUT_CALC_REPROD.out.file
+    .map { row -> [ row[0].group, row[1] ] }
+    .groupTuple(by: [0])
+    .map { row -> [ [id: row[0]], row[1].flatten() ] }
+    .map { row -> [ row[0], row[1], row[1].size() ] }
+    .filter { row -> row[2] > 1 }
+    .map { row -> [ row[0], row[1] ] }
+    .set { ch_peak_bed_group }
+    //ch_peak_bed_group | view
+
+    /*
+    * CHANNEL: Per group, create a channel per one against all combination
+    */
+    ch_peak_bed_group.flatMap{
+        row ->
+        def new_output = []
+        row[1].each{ file ->
+            def files_copy = row[1].collect()
+            files_copy.remove(files_copy.indexOf(file))
+            new_output.add([[id: file.name.split("\\.")[0]], file, files_copy])
+        }
+        new_output
+    }
+    .set { ch_beds_intersect }
+    //EXAMPLE CHANNEL STRUCT: [[META], BED (-a), [BED...n] (-b)]
+    //ch_beds_intersect | view
+
+    /*
+    * MODULE: Find intra-group overlap
+    */
+    BEDTOOLS_INTERSECT (
+        ch_beds_intersect,
+        "bed"
+    )
+    ch_versions = ch_versions.mix(BEDTOOLS_INTERSECT.out.versions)
+    //EXAMPLE CHANNEL STRUCT: [[META], BED]
+    //BEDTOOLS_INTERSECT.out.intersect | view
+
+    /*
+    * MODULE: Use overlap to calculate a peak repro %
+    */
+    CALCULATE_PEAK_REPROD (
+        BEDTOOLS_INTERSECT.out.intersect,
+        peak_reprod_header_multiqc
+    )
+    ch_versions = ch_versions.mix(CALCULATE_PEAK_REPROD.out.versions)
+    //EXAMPLE CHANNEL STRUCT: [[META], TSV]
+    //CALCULATE_PEAK_REPROD.out.tsv
+
+    /*
+    * CHANNEL: Prep for upset input
+    */
+    consensus_peaks_unfiltered
+    .toSortedList { row -> row[0].id }
+    .map { list ->
+        def output = []
+        list.each{ v -> output.add(v[1]) }
+        output
+    }
+    .set { ch_merged_bed_sorted }
+
+    /*
+    * MODULE: Plot upset plots for sample peaks
+    */
+    PLOT_CONSENSUS_PEAKS ( 
+        ch_merged_bed_sorted.ifEmpty([]) 
+    )
+    ch_versions = ch_versions.mix(PLOT_CONSENSUS_PEAKS.out.versions)
+
+    emit:
+    primary_frip_mqc    = PEAK_FRIP.out.frip_mqc              // channel: [ val(meta), [ mqc ] ]
+    primary_count_mqc   = PRIMARY_PEAK_COUNTS.out.count_mqc   // channel: [ val(meta), [ mqc ] ]
+    consensus_count_mqc = CONSENSUS_PEAK_COUNTS.out.count_mqc // channel: [ val(meta), [ mqc ] ]
+    reprod_perc_mqc     = CALCULATE_PEAK_REPROD.out.mqc       // channel: [ val(meta), [ mqc ] ]
+
+    versions = ch_versions // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index 020b347c..62a32dbb 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -2,20 +2,29 @@
  * Uncompress and prepare reference genome files
 */
 
-include { GUNZIP as GUNZIP_FASTA                     } from '../../modules/nf-core/modules/gunzip/main.nf'
-include { GUNZIP as GUNZIP_SPIKEIN_FASTA             } from '../../modules/nf-core/modules/gunzip/main.nf'
-include { GUNZIP as GUNZIP_GTF                       } from '../../modules/nf-core/modules/gunzip/main.nf'
-include { GUNZIP as GUNZIP_BED                       } from '../../modules/nf-core/modules/gunzip/main.nf'
-include { CUSTOM_GETCHROMSIZES as TARGET_CHROMSIZES  } from '../../modules/nf-core/modules/custom/getchromsizes/main.nf'
-include { CUSTOM_GETCHROMSIZES as SPIKEIN_CHROMSIZES } from '../../modules/nf-core/modules/custom/getchromsizes/main.nf'
-include { UNTAR as UNTAR_INDEX_TARGET                } from '../../modules/nf-core/modules/untar/main.nf'
-include { UNTAR as UNTAR_INDEX_SPIKEIN               } from '../../modules/nf-core/modules/untar/main.nf'
-include { BOWTIE2_BUILD as BOWTIE2_BUILD_TARGET      } from '../../modules/nf-core/modules/bowtie2/build/main'
-include { BOWTIE2_BUILD as BOWTIE2_BUILD_SPIKEIN     } from '../../modules/nf-core/modules/bowtie2/build/main'
+include { GUNZIP as GUNZIP_FASTA                               } from '../../modules/nf-core/gunzip/main.nf'
+include { GUNZIP as GUNZIP_SPIKEIN_FASTA                       } from '../../modules/nf-core/gunzip/main.nf'
+include { GUNZIP as GUNZIP_GTF                                 } from '../../modules/nf-core/gunzip/main.nf'
+include { GUNZIP as GUNZIP_BED                                 } from '../../modules/nf-core/gunzip/main.nf'
+include { CUSTOM_GETCHROMSIZES as TARGET_CHROMSIZES            } from '../../modules/nf-core/custom/getchromsizes/main.nf'
+include { CUSTOM_GETCHROMSIZES as SPIKEIN_CHROMSIZES           } from '../../modules/nf-core/custom/getchromsizes/main.nf'
+include { UNTAR as UNTAR_INDEX_TARGET                          } from '../../modules/nf-core/untar/main.nf'
+include { UNTAR as UNTAR_INDEX_SPIKEIN                         } from '../../modules/nf-core/untar/main.nf'
+include { BOWTIE2_BUILD as BOWTIE2_BUILD_TARGET                } from '../../modules/nf-core/bowtie2/build/main'
+include { BOWTIE2_BUILD as BOWTIE2_BUILD_SPIKEIN               } from '../../modules/nf-core/bowtie2/build/main'
+include { TABIX_BGZIPTABIX                                     } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { GTF2BED                                              } from '../../modules/local/gtf2bed'
+include { SAMTOOLS_FAIDX                                       } from '../../modules/nf-core/samtools/faidx/main'
+include { BEDTOOLS_SORT as ANNOTATION_BEDTOOLS_SORT            } from "../../modules/local/for_patch/bedtools/sort/main"
+include { AWK as BLACKLIST_AWK                                 } from "../../modules/local/linux/awk"
+include { BEDTOOLS_INTERSECT as BLACKLIST_BEDTOOLS_INTERSECT   } from "../../modules/nf-core/bedtools/intersect/main"
+include { BEDTOOLS_SORT as BLACKLIST_BEDTOOLS_SORT             } from "../../modules/local/for_patch/bedtools/sort/main"
+include { BEDTOOLS_COMPLEMENT as BLACKLIST_BEDTOOLS_COMPLEMENT } from "../../modules/nf-core/bedtools/complement/main"
 
 workflow PREPARE_GENOME {
     take:
     prepare_tool_indices // list: tools to prepare indices for
+    blacklist            // channel: blacklist file or empty channel
 
     main:
     ch_versions = Channel.empty()
@@ -24,21 +33,22 @@ workflow PREPARE_GENOME {
     * Uncompress genome fasta file if required
     */
     if (params.fasta.endsWith(".gz")) {
-        ch_fasta    = GUNZIP_FASTA ( [ [:], params.fasta ] ).gunzip.map { it[1] }
+        ch_fasta    = GUNZIP_FASTA ( [ [id:"target_fasta"], params.fasta ] ).gunzip
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
     } else {
-        ch_fasta = file(params.fasta)
+        ch_fasta = Channel.from( file(params.fasta) ).map { row -> [[id:"spikein_fasta"], row] }
     }
 
     /*
     * Uncompress spike-in genome fasta file if required
     */
     if (params.spikein_fasta.endsWith(".gz")) {
-        ch_spikein_fasta = GUNZIP_SPIKEIN_FASTA ( [ [:], params.spikein_fasta ] ).gunzip.map { it[1] }
+        ch_spikein_fasta = GUNZIP_SPIKEIN_FASTA ( [ [id:"spikein_fasta"], params.spikein_fasta ] ).gunzip
         ch_versions      = ch_versions.mix(GUNZIP_SPIKEIN_FASTA.out.versions)
     } else {
-        ch_spikein_fasta = file(params.spikein_fasta)
+        ch_spikein_fasta = Channel.from( file(params.spikein_fasta) ).map { row -> [[id:"spikein_fasta"], row] }
     }
+    //ch_spikein_fasta | view
 
     /*
     * Uncompress GTF annotation file
@@ -48,32 +58,72 @@ workflow PREPARE_GENOME {
         ch_gtf      = GUNZIP_GTF ( [ [:], params.gtf ] ).gunzip.map { it[1] }
         ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
     } else {
-        ch_gtf = file(params.gtf)
+        ch_gtf = Channel.from( file(params.gtf) )
     }
 
-    /*
-    * Uncompress BED annotation file
-    */
     ch_gene_bed = Channel.empty()
     if (params.gene_bed){
+        /*
+        * Uncompress BED annotation file
+        */
         if (params.gene_bed.endsWith(".gz")) {
             ch_gene_bed = GUNZIP_BED ( [ [:], params.gene_bed ] ).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_BED.out.versions)
         } else {
-            ch_gene_bed = file(params.gene_bed)
+            ch_gene_bed = Channel.from( file(params.gene_bed) )
+        }
+    } else {
+        /*
+        * Create GTF bed file if needed
+        */
+        GTF2BED ( ch_gtf )
+        ch_gene_bed = GTF2BED.out.bed
+        ch_versions = ch_versions.mix(GTF2BED.out.versions)
+    }
+
+    /*
+    * Sort and index the bed annotation file
+    */
+    ch_tabix = ch_gene_bed.map { 
+        row -> [ [ id:row.getName() ] , row ] 
+    }
+
+    if (params.gene_bed && params.gene_bed.endsWith(".gz")) {
+        ch_tabix = ch_tabix.map {
+            row ->
+                new_id = row[0].id.split("\\.")[0]
+                [ [ id: new_id ] , row[1] ] 
         }
     }
 
+    ANNOTATION_BEDTOOLS_SORT (
+        ch_tabix,
+        "bed",
+        []
+    )
+
+    TABIX_BGZIPTABIX (
+        ANNOTATION_BEDTOOLS_SORT.out.sorted
+    )
+    ch_gene_bed_index = TABIX_BGZIPTABIX.out.gz_tbi
+    ch_versions       = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
+
+    /*
+    * Index genome fasta file
+    */
+    ch_fasta_index = SAMTOOLS_FAIDX ( ch_fasta ).fai
+    ch_versions    = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+
     /*
     * Create chromosome sizes file
     */
-    ch_chrom_sizes = TARGET_CHROMSIZES ( ch_fasta ).sizes
+    ch_chrom_sizes = TARGET_CHROMSIZES ( ch_fasta ).sizes.map{ it[1] }
     ch_versions    = ch_versions.mix(TARGET_CHROMSIZES.out.versions)
 
     /*
     * Create chromosome sizes file for spike_in
     */
-    ch_spikein_chrom_sizes = SPIKEIN_CHROMSIZES ( ch_spikein_fasta ).sizes
+    ch_spikein_chrom_sizes = SPIKEIN_CHROMSIZES ( ch_spikein_fasta ).sizes.map{ it[1] }
 
     /*
     * Uncompress Bowtie2 index or generate from scratch if required for both genomes
@@ -107,12 +157,59 @@ workflow PREPARE_GENOME {
         }
     }
 
+    /*
+    * Use blacklist to create include regions for genome
+    */
+    ch_genome_include_regions = Channel.empty()
+    if (params.blacklist) {
+        // Create bedfile from chrom sizes file
+        BLACKLIST_AWK (
+            ch_chrom_sizes.map {row -> [ [id: "chromsizes"], row ]}
+        )
+        ch_versions = ch_versions.mix(BLACKLIST_AWK.out.versions)
+
+        // Create intersect channel between the chrom sizes bed and the blacklist bed
+        // This reduces the blacklist file down to the 
+        ch_blacklist_intersect = blacklist
+            .map {row -> [ [id: "blacklist"], row ]}
+            .combine( BLACKLIST_AWK.out.file )
+            .map {row -> [ row[0], row[1], row[3] ]}
+        //ch_blacklist_intersect | view
+
+        // Intersect blacklist with available chromosomes
+        // this prevents error in the next two processes
+        BLACKLIST_BEDTOOLS_INTERSECT(
+            ch_blacklist_intersect,
+            "filtered.bed"
+        )
+        ch_versions = ch_versions.mix(BLACKLIST_BEDTOOLS_INTERSECT.out.versions)
+
+        // Sort the bed file
+        BLACKLIST_BEDTOOLS_SORT(
+            BLACKLIST_BEDTOOLS_INTERSECT.out.intersect,
+            "sorted.bed",
+            ch_chrom_sizes
+        )
+        ch_versions = ch_versions.mix(BLACKLIST_BEDTOOLS_SORT.out.versions)
+
+        // Find compliment of blacklist to show allowed regions
+        BLACKLIST_BEDTOOLS_COMPLEMENT(
+            BLACKLIST_BEDTOOLS_SORT.out.sorted,
+            ch_chrom_sizes
+        )
+        ch_genome_include_regions = BLACKLIST_BEDTOOLS_COMPLEMENT.out.bed
+        ch_versions               = ch_versions.mix(BLACKLIST_BEDTOOLS_COMPLEMENT.out.versions)
+    }
+
     emit:
     fasta                  = ch_fasta                    // path: genome.fasta
+    fasta_index            = ch_fasta_index              // path: genome.fai
     chrom_sizes            = ch_chrom_sizes              // path: genome.sizes
     spikein_chrom_sizes    = ch_spikein_chrom_sizes      // path: genome.sizes
     gtf                    = ch_gtf                      // path: genome.gtf
     bed                    = ch_gene_bed                 // path: genome.bed
+    bed_index              = ch_gene_bed_index           // path: genome.bed_index
+    allowed_regions        = ch_genome_include_regions   // path: genome.regions
     bowtie2_index          = ch_bt2_index                // path: bt2/index/
     bowtie2_spikein_index  = ch_bt2_spikein_index        // path: bt2/index/
 
diff --git a/subworkflows/nf-core/bam_sort_samtools.nf b/subworkflows/nf-core/bam_sort_samtools.nf
index 062f05cc..0b84501d 100644
--- a/subworkflows/nf-core/bam_sort_samtools.nf
+++ b/subworkflows/nf-core/bam_sort_samtools.nf
@@ -2,8 +2,8 @@
  * Sort, index BAM file and run samtools stats, flagstat and idxstats
  */
 
-include { SAMTOOLS_SORT      } from '../../modules/nf-core/modules/samtools/sort/main'
-include { SAMTOOLS_INDEX     } from '../../modules/nf-core/modules/samtools/index/main'
+include { SAMTOOLS_SORT      } from '../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX     } from '../../modules/nf-core/samtools/index/main'
 include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools'
 
 workflow BAM_SORT_SAMTOOLS {
diff --git a/subworkflows/nf-core/bam_stats_samtools.nf b/subworkflows/nf-core/bam_stats_samtools.nf
index e47163eb..87215687 100644
--- a/subworkflows/nf-core/bam_stats_samtools.nf
+++ b/subworkflows/nf-core/bam_stats_samtools.nf
@@ -2,9 +2,9 @@
  * Run SAMtools stats, flagstat and idxstats
  */
 
-include { SAMTOOLS_STATS    } from '../../modules/nf-core/modules/samtools/stats/main'
-include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/modules/samtools/idxstats/main'
-include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/modules/samtools/flagstat/main'
+include { SAMTOOLS_STATS    } from '../../modules/nf-core/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main'
 
 workflow BAM_STATS_SAMTOOLS {
     take:
@@ -14,13 +14,13 @@ workflow BAM_STATS_SAMTOOLS {
     ch_versions = Channel.empty()
 
     SAMTOOLS_STATS    ( ch_bam_bai, [] )
-    ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
+    ch_versions = ch_versions.mix( SAMTOOLS_STATS.out.versions.first() )
 
     SAMTOOLS_FLAGSTAT ( ch_bam_bai )
-    ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first())
+    ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions.first() )
 
     SAMTOOLS_IDXSTATS ( ch_bam_bai )
-    ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first())
+    ch_versions = ch_versions.mix( SAMTOOLS_IDXSTATS.out.versions.first() )
 
     emit:
     stats    = SAMTOOLS_STATS.out.stats       // channel: [ val(meta), [ stats ] ]
diff --git a/subworkflows/nf-core/deeptools_qc.nf b/subworkflows/nf-core/deeptools_qc.nf
new file mode 100644
index 00000000..7a03d8f9
--- /dev/null
+++ b/subworkflows/nf-core/deeptools_qc.nf
@@ -0,0 +1,108 @@
+/*
+ * Perform full suite of deep tools analysis on bam files
+*/
+
+include { DEEPTOOLS_MULTIBAMSUMMARY } from '../../modules/local/deeptools/multibamsummary/main'
+include { DEEPTOOLS_PLOTCORRELATION } from '../../modules/local/deeptools/plotcorrelation/main'
+include { DEEPTOOLS_PLOTPCA         } from '../../modules/local/deeptools/plotpca/main'
+include { DEEPTOOLS_PLOTFINGERPRINT } from '../../modules/nf-core/deeptools/plotfingerprint/main'
+
+workflow DEEPTOOLS_QC {
+    take:
+    bam // channel: [ val(meta), [ bam ] ]
+    bai // channel: [ val(meta), [ bai ] ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    /*
+    * CHANNEL: Filter bams for target only
+    */
+    bam.filter { it -> it[0].is_control == false }
+    .set { ch_bam_target }
+    //ch_bam_target | view
+
+    /*
+    * CHANNEL: Filter bais for target only
+    */
+    bai.filter { it -> it[0].is_control == false }
+    .set { ch_bai_target }
+    //ch_bai_target | view
+
+    /*
+    * CHANNEL: Combine bam and bai files on id
+    */
+    ch_bam_target.map { row -> [row[0].id, row ].flatten()}
+    .join ( ch_bai_target.map { row -> [row[0].id, row ].flatten()} )
+    .map { row -> [row[1], row[2], row[4]] }
+    .set { ch_bam_bai }
+    // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI]
+    //ch_bam_bai | view
+
+    /*
+    * CHANNEL: Get list of sample ids
+    */
+    ch_bam_target.map { row -> [row[0].id] }
+    .collect()
+    .map { row -> [row] }
+    .set { ch_ids }
+    //ch_ids | view
+
+    /*
+    * CHANNEL: Combine bam and bai files into one list
+    * if we only have one file then cancel correlation and PCA
+    */
+    ch_bam_target.map { row -> [row[1]] }
+    .collect()
+    .map { row -> [row] } 
+    .combine( ch_bai_target.map { row -> [row[1]] }.collect().map { row -> [row] } )
+    .combine( ch_ids )
+    .map { row -> [[id: 'all_target_bams'], row[0], row[1], row[2], row[1].size()] }
+    .filter { row -> row[4] > 1 }
+    .map { row -> [row[0], row[1], row[2], row[3]] }
+    .set { ch_bam_bai_all }
+    //ch_bam_bai_all | view
+
+    /*
+    * MODULE: Summarise bams into bins
+    */
+    DEEPTOOLS_MULTIBAMSUMMARY (
+        ch_bam_bai_all
+    )
+    ch_versions = ch_versions.mix(DEEPTOOLS_MULTIBAMSUMMARY.out.versions)
+    //DEEPTOOLS_MULTIBAMSUMMARY.out.matrix | view
+
+    /*
+    * MODULE: Plot correlation matrix
+    */
+    DEEPTOOLS_PLOTCORRELATION (
+        DEEPTOOLS_MULTIBAMSUMMARY.out.matrix
+    )
+    ch_versions = ch_versions.mix(DEEPTOOLS_PLOTCORRELATION.out.versions)
+    //DEEPTOOLS_MULTIBAMSUMMARY.out.matrix | view
+
+    /*
+    * MODULE: Plot PCA's
+    */
+    DEEPTOOLS_PLOTPCA (
+        DEEPTOOLS_MULTIBAMSUMMARY.out.matrix
+    )
+    ch_versions = ch_versions.mix(DEEPTOOLS_PLOTPCA.out.versions)
+    //DEEPTOOLS_PLOTPCA.out.matrix | view
+
+    /*
+    * MODULE: Plot Fingerprint
+    */
+    DEEPTOOLS_PLOTFINGERPRINT (
+        ch_bam_bai
+    )
+    ch_versions = ch_versions.mix(DEEPTOOLS_PLOTFINGERPRINT.out.versions)
+    //DEEPTOOLS_PLOTFINGERPRINT.out.matrix | view
+
+    emit:
+    correlation_matrix = DEEPTOOLS_PLOTCORRELATION.out.matrix
+    pca_data           = DEEPTOOLS_PLOTPCA.out.tab
+    fingerprint_matrix = DEEPTOOLS_PLOTFINGERPRINT.out.matrix
+
+    versions               = ch_versions                 // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/mark_duplicates_picard.nf b/subworkflows/nf-core/mark_duplicates_picard.nf
index 2dd25e80..1b8d85b2 100644
--- a/subworkflows/nf-core/mark_duplicates_picard.nf
+++ b/subworkflows/nf-core/mark_duplicates_picard.nf
@@ -2,14 +2,13 @@
  * Picard MarkDuplicates, sort, index BAM file and run samtools stats, flagstat and idxstats
  */
 
-include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/modules/picard/markduplicates/main'
-include { SAMTOOLS_INDEX        } from '../../modules/nf-core/modules/samtools/index/main'
-include { BAM_STATS_SAMTOOLS    } from './bam_stats_samtools'
+include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main'
+include { BAM_SORT_SAMTOOLS     } from './bam_sort_samtools'
 
 workflow MARK_DUPLICATES_PICARD {
     take:
     bam            // channel: [ val(meta), [ bam ] ]
-    process_target //boolean
+    process_target // boolean
 
     main:
     /*
@@ -22,7 +21,7 @@ workflow MARK_DUPLICATES_PICARD {
         PICARD_MARKDUPLICATES ( bam )
         ch_bam      = PICARD_MARKDUPLICATES.out.bam
         metrics     = PICARD_MARKDUPLICATES.out.metrics
-        ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
+        ch_versions = ch_versions.mix( PICARD_MARKDUPLICATES.out.versions )
     }
     else { // Split out control files and run only on these
         bam.branch { it ->
@@ -34,40 +33,36 @@ workflow MARK_DUPLICATES_PICARD {
         //ch_split.control | view
 
         PICARD_MARKDUPLICATES ( ch_split.control )
-        ch_bam      = PICARD_MARKDUPLICATES.out.bam.mix ( ch_split.target )
+
+        // Prevents issues with resume with the branch elements coming in the wrong order
+        ch_sorted_targets = ch_split.target
+            .toSortedList { row -> row[0].id }
+            .flatMap()
+
+        ch_sorted_controls = PICARD_MARKDUPLICATES.out.bam
+            .toSortedList { row -> row[0].id }
+            .flatMap()
+
+        ch_bam      = ch_sorted_targets.concat ( ch_sorted_controls )
         metrics     = PICARD_MARKDUPLICATES.out.metrics
-        ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
+        ch_versions = ch_versions.mix( PICARD_MARKDUPLICATES.out.versions )
     }
     //ch_bam | view
 
     /*
-    * Index BAM file
-    */
-    SAMTOOLS_INDEX ( ch_bam )
-    ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
-
-    // Join bam/bai
-    ch_bam
-        .map { row -> [row[0].id, row ].flatten()}
-        .join ( SAMTOOLS_INDEX.out.bai.map { row -> [row[0].id, row ].flatten()} )
-        .map { row -> [row[1], row[2], row[4]] }
-        .set { ch_bam_bai }
-    //ch_bam_bai | view
-
-    /*
-    * Run samtools stats, flagstat and idxstats
+    * WORKFLOW: Re sort and index all the bam files + calculate stats
     */
-    BAM_STATS_SAMTOOLS ( ch_bam_bai )
-    ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
+    BAM_SORT_SAMTOOLS ( 
+        ch_bam 
+    )
 
     emit:
-    bam      = ch_bam                            // channel: [ val(meta), [ bam ] ]
-    metrics                                      // channel: [ val(meta), [ metrics ] ]
-
-    bai      = SAMTOOLS_INDEX.out.bai            // channel: [ val(meta), [ bai ] ]
-    stats    = BAM_STATS_SAMTOOLS.out.stats      // channel: [ val(meta), [ stats ] ]
-    flagstat = BAM_STATS_SAMTOOLS.out.flagstat   // channel: [ val(meta), [ flagstat ] ]
-    idxstats = BAM_STATS_SAMTOOLS.out.idxstats   // channel: [ val(meta), [ idxstats ] ]
+    bam      = BAM_SORT_SAMTOOLS.out.bam        // channel: [ val(meta), [ bam ] ]
+    bai      = BAM_SORT_SAMTOOLS.out.bai        // channel: [ val(meta), [ bai ] ]
+    stats    = BAM_SORT_SAMTOOLS.out.stats      // channel: [ val(meta), [ stats ] ]
+    flagstat = BAM_SORT_SAMTOOLS.out.flagstat   // channel: [ val(meta), [ flagstat ] ]
+    idxstats = BAM_SORT_SAMTOOLS.out.idxstats   // channel: [ val(meta), [ idxstats ] ]
+    metrics                                     // channel: [ val(meta), [ metrics ] ]
 
-    versions = ch_versions                       // channel: [ versions.yml ]
+    versions = ch_versions                      // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/prepare_peakcalling.nf b/subworkflows/nf-core/prepare_peakcalling.nf
index c332da4e..13578d1e 100644
--- a/subworkflows/nf-core/prepare_peakcalling.nf
+++ b/subworkflows/nf-core/prepare_peakcalling.nf
@@ -2,11 +2,11 @@
  * Convert bam files to bedgraph and bigwig with apropriate normalisation
  */
 
-include { BEDTOOLS_GENOMECOV    } from "../../modules/nf-core/modules/bedtools/genomecov/main"
-include { DEEPTOOLS_BAMCOVERAGE } from "../../modules/local/modules/deeptools/bamcoverage/main"
-include { BEDTOOLS_SORT         } from "../../modules/nf-core/modules/bedtools/sort/main"
-include { UCSC_BEDCLIP          } from "../../modules/nf-core/modules/ucsc/bedclip/main"
-include { UCSC_BEDGRAPHTOBIGWIG } from "../../modules/nf-core/modules/ucsc/bedgraphtobigwig/main"
+include { BEDTOOLS_GENOMECOV    } from "../../modules/nf-core/bedtools/genomecov/main"
+include { DEEPTOOLS_BAMCOVERAGE } from "../../modules/local/deeptools/bamcoverage/main"
+include { BEDTOOLS_SORT         } from "../../modules/local/for_patch/bedtools/sort/main"
+include { UCSC_BEDCLIP          } from "../../modules/nf-core/ucsc/bedclip/main"
+include { UCSC_BEDGRAPHTOBIGWIG } from "../../modules/nf-core/ucsc/bedgraphtobigwig/main"
 
 workflow PREPARE_PEAKCALLING {
     take:
@@ -14,58 +14,53 @@ workflow PREPARE_PEAKCALLING {
     ch_bai         // channel: [ val(meta), [ bai ] ]
     ch_chrom_sizes // channel: [ sizes ]
     ch_dummy_file  // channel: [ dummy ]
-    norm_mode      // value: ["Spikein", "RPKM", "CPM", "BPM", "RPGC", "None" ]
+    norm_mode      // value:   ["Spikein", "RPKM", "CPM", "BPM", "RPGC", "None" ]
+    metadata       // channel  [ csv ]
 
     main:
     ch_versions = Channel.empty()
-    ch_bam_out  = Channel.empty()
     ch_bedgraph = Channel.empty()
 
     if (norm_mode == "Spikein") {
+        /*
+        * CHANNEL: Load up alignment metadata into channel
+        */
+        metadata.splitCsv ( header:true, sep:"," )
+            .map { row -> [ row[0].id, row[1] ]}
+            .set { ch_metadata }
+        //ch_metadata | view
+
         /*
         * CHANNEL: Calculate scale factor for each sample based on a constant devided by the number
         *          of reads aligned to the spike-in genome.
         */
-        ch_bam
+        ch_bam.map { row -> [ row[0].id, row[0], row[1] ]}
+            .join ( ch_metadata )
             .map { row ->
-                def denominator = row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger()
-                [ row[0].id, params.normalisation_c / (denominator != 0 ? denominator : 1) ]
+                def denominator = row[3].find{ it.key == "bt2_total_aligned" }?.value.toInteger()
+                [ row[1], row[2], params.normalisation_c / (denominator != 0 ? denominator : params.normalisation_c) ]
             }
-        .set { ch_scale_factor }
+            .set { ch_bam_scale_factor }
         // EXAMPLE CHANNEL STRUCT: [id, scale_factor]
-        //ch_scale_factor | view
+        //ch_bam_scale_factor | view
     }
     else if (norm_mode == "None") {
         /*
         * CHANNEL: Assign scale factor of 1
         */
-        ch_bam
-            .map { row ->
-                [ row[0].id, 1 ]
+        ch_bam.map { row ->
+                [ row[0], row[1], 1 ]
             }
-        .set { ch_scale_factor }
+            .set { ch_bam_scale_factor }
+        //ch_bam_scale_factor | view
     }
 
     if (norm_mode == "Spikein" || norm_mode == "None") {
-        /*
-        * CHANNEL: Create a channel with the scale factor as a seperate value
-        */
-        ch_bam
-            .map { row -> [row[0].id, row ].flatten()}
-            .join ( ch_scale_factor )
-            .map { row -> row[1..(row.size() - 1)] }
-            .map { row ->
-                row[0].put("scale_factor", row[2])
-                [ row[0], row[1], row[2] ] }
-        .set { ch_bam_scale }
-        //EXAMPLE CHANNEL STRUCT: [[META + scale_factor:10000], BAM, SCALE_FACTOR]
-        //ch_bam_scale | view
-
         /*
         * MODULE: Convert bam files to bedgraph
         */
         BEDTOOLS_GENOMECOV (
-            ch_bam_scale,
+            ch_bam_scale_factor,
             ch_dummy_file,
             "bedGraph"
         )
@@ -73,15 +68,6 @@ workflow PREPARE_PEAKCALLING {
         ch_bedgraph = BEDTOOLS_GENOMECOV.out.genomecov
         //EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
         //BEDTOOLS_GENOMECOV.out.genomecov | view
-
-        /*
-        * CHANNEL: Add the scale factor values to the main meta-data stream
-        */
-        ch_bam_scale
-            .map { row -> [ row[0], row[1] ] }
-        .set { ch_bam_out }
-        //EXAMPLE CHANNEL STRUCT: [[META], BAM]
-        //ch_samtools_bam | view
     } else {
         /*
         * CHANNEL: Combine bam and bai files on id
@@ -144,9 +130,6 @@ workflow PREPARE_PEAKCALLING {
         ch_bedgraph = DEEPTOOLS_BAMCOVERAGE.out.bedgraph
         // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI]
         //ch_bedgraph | view
-
-        // Dont assign any new meta data
-        ch_bam_out = ch_bam
     }
 
     /*
@@ -154,7 +137,8 @@ workflow PREPARE_PEAKCALLING {
     */
     BEDTOOLS_SORT (
         ch_bedgraph,
-        "bedGraph"
+        "bedGraph",
+        []
     )
     ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions)
 
@@ -181,7 +165,6 @@ workflow PREPARE_PEAKCALLING {
     //UCSC_BEDGRAPHTOBIGWIG.out.bigwig | view
 
     emit:
-    bam      = ch_bam_out                       // channel: [ val(meta), [ bam ] ]
     bedgraph = UCSC_BEDCLIP.out.bedgraph        // channel: [ val(meta), [ bedgraph ] ]
     bigwig   = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bigwig ] ]
     versions = ch_versions                      // channel: [ versions.yml ]
diff --git a/subworkflows/nf-core/samtools_view_sort_stats.nf b/subworkflows/nf-core/samtools_view_sort_stats.nf
index 7071062b..cda5a59f 100644
--- a/subworkflows/nf-core/samtools_view_sort_stats.nf
+++ b/subworkflows/nf-core/samtools_view_sort_stats.nf
@@ -2,21 +2,22 @@
  * Run bam files through samtools view and reindex and calc stats
  */
 
-include { SAMTOOLS_VIEW      } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_SORT      } from '../../modules/nf-core/modules/samtools/sort/main'
-include { SAMTOOLS_INDEX     } from '../../modules/nf-core/modules/samtools/index/main'
+include { SAMTOOLS_VIEW      } from '../../modules/local/for_patch/samtools/view/main'
+include { SAMTOOLS_SORT      } from '../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX     } from '../../modules/nf-core/samtools/index/main'
 include { BAM_STATS_SAMTOOLS } from '../nf-core/bam_stats_samtools'
 
 workflow SAMTOOLS_VIEW_SORT_STATS {
     take:
-    bam // channel: [ val(meta), [ bam ] ]
+    bam       // channel: [ val(meta), [ bam ] ]
+    regions   // channel: [ regions ]
 
     main:
     ch_versions = Channel.empty()
     /*
      * Filter BAM file
      */
-    SAMTOOLS_VIEW ( bam.map{ row -> [ row[0], row[1], [] ] }, [] )
+    SAMTOOLS_VIEW ( bam.map{ row -> [ row[0], row[1], [], ] }, [], regions )
     ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first())
 
     /*
@@ -45,5 +46,5 @@ workflow SAMTOOLS_VIEW_SORT_STATS {
     stats    = BAM_STATS_SAMTOOLS.out.stats     // channel: [ val(meta), [ stats ] ]
     flagstat = BAM_STATS_SAMTOOLS.out.flagstat  // channel: [ val(meta), [ flagstat ] ]
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats  // channel: [ val(meta), [ idxstats ] ]
-    versions = ch_versions                    // channel: [ versions.yml ]
+    versions = ch_versions                      // channel: [ versions.yml ]
 }
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index 8c62e29e..79cb9380 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -1,10 +1,23 @@
 params {
     outdir = "results/"
     publish_dir_mode = "copy"
+      enable_conda = false
+    singularity_pull_docker_container = false
 }
 
 process {
   cpus = 2
   memory = 6.GB
   time = 6.h
-}
\ No newline at end of file
+}
+
+if ("$PROFILE" == "singularity") {
+    singularity.enabled = true
+    singularity.autoMounts = true
+} else if ("$PROFILE" == "conda") {
+    params.enable_conda = true
+} else {
+    docker.enabled = true
+    docker.userEmulation = true
+    docker.runOptions = "--platform linux/x86_64"
+}
diff --git a/tests/test_01_genome_options.yml b/tests/test_01_genome_options.yml
new file mode 100644
index 00000000..14082bde
--- /dev/null
+++ b/tests/test_01_genome_options.yml
@@ -0,0 +1,34 @@
+- name: test_param_check_custom_genome_blacklist
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz --blacklist ./assets/blacklists/hg38-blacklist.bed -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_noblacklist
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_nobed
+  command: nextflow run main.nf -profile docker,test --only_genome -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_gtf
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr7-genes.gtf -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_gtf_gz
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_bed
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz --gene_bed https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr7-genes.bed -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
+
+- name: test_param_check_custom_genome_bed_gz
+  command: nextflow run main.nf -profile docker,test_fasta_only --only_genome --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz --gene_bed https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr7-genes.bed.gz -c tests/config/nextflow.config
+  tags:
+    - test_genome_options
diff --git a/tests/test_samplesheet_check.yml b/tests/test_02_samplesheet_check.yml
similarity index 58%
rename from tests/test_samplesheet_check.yml
rename to tests/test_02_samplesheet_check.yml
index 856493c0..72329782 100644
--- a/tests/test_samplesheet_check.yml
+++ b/tests/test_02_samplesheet_check.yml
@@ -1,13 +1,13 @@
 # Test incorrect header
 - name: test_samplesheet_header_error
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/header_error.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/header_error.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test use_control false when noigg in sample sheet does not produce error
 - name: test_samplesheet_noigg_pos
-  command: nextflow run main.nf -profile docker,test --only_input true --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/no_igg.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/no_igg.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   files:
@@ -15,7 +15,7 @@
 
 # Test use_control false when control in sample sheet does not produce error
 - name: test_samplesheet_noigg_pos_ctrl_neg
-  command: nextflow run main.nf -profile docker,test --only_input true --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   files:
@@ -23,7 +23,7 @@
 
 # Test use_control true when noigg in sample sheet does produce error
 - name: test_samplesheet_noigg_neg
-  command: nextflow run main.nf -profile docker,test --only_input true --use_control true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/no_igg.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --use_control true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/no_igg.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
@@ -38,91 +38,91 @@
 
 # Test invalid number of columns in row
 - name: test_samplesheet_invalid_cols_in_row
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/invalid_column_in_row.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/invalid_column_in_row.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test group is blank
 - name: test_samplesheet_group_is_blank
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_is_blank.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_is_blank.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test group has spaces
 - name: test_samplesheet_group_has_spaces
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_has_spaces.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_has_spaces.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test control has spaces
 - name: test_samplesheet_control_has_spaces
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_has_spaces.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_has_spaces.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test group equals control
 - name: test_samplesheet_group_equals_control
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_equals_control.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/group_equals_control.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test negative replicate number
 - name: test_samplesheet_neg_rep
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/negative_rep_num.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/negative_rep_num.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test replicate number does not start at 1
 - name: test_samplesheet_rep_not_start_one
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/rep_not_start_one.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/rep_not_start_one.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test fastq ext incorrect
 - name: test_samplesheet_fastq_ext_error
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/fastq_ext_error.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/fastq_ext_error.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test fastq path spaces
 - name: test_samplesheet_fastq_path_spaces_error
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/fastq_file_spaces.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/fastq_file_spaces.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test duplicate rows
 - name: test_samplesheet_dup_rows
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/duplicate_rows.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/duplicate_rows.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test control not exist
 - name: test_samplesheet_ctrl_not_exist
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_not_exist.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_not_exist.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test control with control
 - name: test_samplesheet_ctrl_with_ctrl
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_with_control.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/control_with_control.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   exit_code: 1
 
 # Test small sample sheet
 - name: test_samplesheet_small
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   files:
@@ -130,7 +130,7 @@
 
 # Test small tech reps
 - name: test_samplesheet_small_tech_reps
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small-tech-reps.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small-tech-reps.csv -c tests/config/nextflow.config
   tags:
     - test_samplesheet
   files:
@@ -138,55 +138,55 @@
 
 # Test noigg small
 - name: test_samplesheet_small_noigg
-  command: nextflow run main.nf -profile docker,test --only_input true --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-noigg-small.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --use_control false --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-noigg-small.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test all
 - name: test_samplesheet_all
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test all small
 - name: test_samplesheet_all_small
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-small.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-small.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test all multi-rep
 - name: test_samplesheet_all_multi_rep
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test all multi-rep single-ctrl
 - name: test_samplesheet_multi_rep_single_ctrl
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test all multi-rep multi-single-ctrl
 - name: test_samplesheet_multi_rep_multi_single_ctrl
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
 
 # Test legacy 1_0 samplesheet
 - name: test_samplesheet_legacy_1_0
-  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/legacy/1_0_samplesheet.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_input --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/unit_tests/legacy/1_0_samplesheet.csv -c tests/config/nextflow.config
   tags:
-    - test_samplesheet
+    - test_samplesheet_2
   exit_code: 1
diff --git a/tests/test_03_ailgnment_filtering.yml b/tests/test_03_ailgnment_filtering.yml
new file mode 100644
index 00000000..f464c18b
--- /dev/null
+++ b/tests/test_03_ailgnment_filtering.yml
@@ -0,0 +1,11 @@
+- name: test_filtering_noqfilter
+  command: nextflow run main.nf -profile docker,test --only_filtering true -c tests/config/nextflow.config
+  tags:
+    - test_filtering
+    - test_filtering_noqfilter
+
+- name: test_filtering_withqfilter
+  command: nextflow run main.nf -profile docker,test --only_filtering true --minimum_alignment_q_score 10 -c tests/config/nextflow.config
+  tags:
+    - test_filtering
+    - test_filtering_withqfilter
diff --git a/tests/test_bam_scaling.yml b/tests/test_04_bam_scaling.yml
similarity index 58%
rename from tests/test_bam_scaling.yml
rename to tests/test_04_bam_scaling.yml
index 403f3e17..ad730804 100644
--- a/tests/test_bam_scaling.yml
+++ b/tests/test_04_bam_scaling.yml
@@ -1,69 +1,55 @@
 - name: test_bam_scale_none
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode None -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode None -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_none
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	1"
 
 - name: test_bam_scale_spikein
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode Spikein -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode Spikein -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_spikein
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	10000"
 
 - name: test_bam_scale_cpm
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode CPM -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_cpm
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	1607.72"
 
 - name: test_bam_scale_rpkm
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode RPKM -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode RPKM -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_rpkm
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	1.60772e+06"
 
 - name: test_bam_scale_bpm
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode BPM -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode BPM -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_bpm
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	1607.72"
 
 - name: test_bam_scale_cpm_iggscale
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM --igg_scale_factor 0.1 -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_preseq --skip_multiqc --normalisation_mode CPM --igg_scale_factor 0.1 -c tests/config/nextflow.config
   tags:
     - test_bam_scale
     - test_bam_scale_cpm_iggscale
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
-      contains:
-        - "chr20	171984	172009	1607.72"
     - path: results/03_peak_calling/01_bam_to_bedgraph/igg_ctrl_R1.sorted.bedGraph
-      contains:
-        - "chr20	606391	606415	285.714"
 
 - name: test_normalisation_mode_invalid
   command:
-    nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --normalisation_mode test -c tests/config/nextflow.config
+    nextflow run main.nf -profile docker,test --only_peak_calling --normalisation_mode test -c tests/config/nextflow.config
     - test_bam_scale
     - test_bam_scale_invalid
   exit_code: 1
diff --git a/tests/test_05_peak_callers.yml b/tests/test_05_peak_callers.yml
new file mode 100644
index 00000000..c18d295b
--- /dev/null
+++ b/tests/test_05_peak_callers.yml
@@ -0,0 +1,79 @@
+- name: test_peak_callers_seacr
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller seacr -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_seacr
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+
+- name: test_peak_callers_macs2
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller macs2 -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_macs2
+  files:
+    - path: results/03_peak_calling/04_called_peaks/macs2/h3k27me3_R1.macs2_peaks.narrowPeak
+
+- name: test_peak_callers_macs2_broad_peak
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller macs2 --macs2_narrow_peak false -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_macs2
+  files:
+    - path: results/03_peak_calling/04_called_peaks/macs2/h3k27me3_R1.macs2_peaks.broadPeak
+
+- name: test_peak_callers_invalid_name
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller test -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_invalid
+  exit_code: 1
+
+- name: test_peak_callers_seacr_macs2
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller seacr,macs2 -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_seacr_macs2
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/macs2/h3k27me3_R1.macs2_peaks.narrowPeak
+
+- name: test_peak_callers_macs2_seacr
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller macs2,seacr -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_macs2_seacr
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/macs2/h3k27me3_R1.macs2_peaks.narrowPeak
+
+- name: test_peak_callers_seacr_macs2_noigg
+  command: nextflow run main.nf -profile docker,test_no_control --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller seacr,macs2 -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_seacr_macs2_noigg
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/macs2/h3k27me3_R1.macs2_peaks.narrowPeak
+
+- name: test_peak_callers_seacr_single_ctrl_multi_rep
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_ctrl_tests
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k4me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k4me3_R2.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R2.seacr.peaks.stringent.bed
+
+- name: test_peak_callers_seacr_multi_single_ctrl_multi_rep
+  command: nextflow run main.nf -profile docker,test --only_peak_calling --skip_fastqc --skip_removeduplicates --skip_multiqc --skip_preseq --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
+  tags:
+    - test_peak_callers
+    - test_peak_callers_ctrl_tests
+  files:
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k4me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k4me3_R2.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R2.seacr.peaks.stringent.bed
diff --git a/tests/test_06_consenseus_peaks.yml b/tests/test_06_consenseus_peaks.yml
new file mode 100644
index 00000000..4cee6557
--- /dev/null
+++ b/tests/test_06_consenseus_peaks.yml
@@ -0,0 +1,26 @@
+- name: test_consensus_peaks_group
+  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling --skip_fastqc --skip_multiqc --skip_preseq --consensus_peak_mode group -c tests/config/nextflow.config
+  tags:
+    - test_consensus_peaks
+    - test_consensus_peaks_group
+  files:
+    - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peak_counts.bed
+    - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.awk.bed
+    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peak_counts.bed
+    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.awk.bed
+
+- name: test_consensus_peaks_all
+  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling --skip_fastqc --skip_multiqc --skip_preseq --consensus_peak_mode all -c tests/config/nextflow.config
+  tags:
+    - test_consensus_peaks
+    - test_consensus_peaks_all
+  files:
+    - path: results/03_peak_calling/05_consensus_peaks/all_samples.consensus.peaks.awk.bed
+    - path: results/03_peak_calling/05_consensus_peaks/all_samples.consensus.peak_counts.bed
+
+- name: test_consensus_peaks_invalid
+  command:
+    nextflow run main.nf -profile docker,test_full_small --only_peak_calling --skip_fastqc --skip_multiqc --skip_preseq --consensus_peak_mode test -c tests/config/nextflow.config
+    - test_consensus_peaks
+    - test_consensus_peaks_invalid
+  exit_code: 1
diff --git a/tests/test_consenseus_peaks.yml b/tests/test_consenseus_peaks.yml
deleted file mode 100644
index aa6dacd8..00000000
--- a/tests/test_consenseus_peaks.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: test_conseneus_peaks_group
-  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode group -c tests/config/nextflow.config
-  tags:
-    - test_conseneus_peaks
-    - test_conseneus_peaks_group
-  files:
-    - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.bed
-    - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.filtered.awk.bed
-    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.bed
-    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.filtered.awk.bed
-
-- name: test_conseneus_peaks_all
-  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode all -c tests/config/nextflow.config
-  tags:
-    - test_conseneus_peaks
-    - test_conseneus_peaks_all
-  files:
-    - path: results/03_peak_calling/05_consensus_peaks/all_samples.awk.bed
-    - path: results/03_peak_calling/05_consensus_peaks/all_samples.consensus.peaks.bed
-
-- name: test_conseneus_peaks_invalid
-  command:
-    nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode test -c tests/config/nextflow.config
-    - test_conseneus_peaks
-    - test_conseneus_peaks_invalid
-  exit_code: 1
diff --git a/tests/test_param_check.yml b/tests/test_param_check.yml
deleted file mode 100644
index f97f308d..00000000
--- a/tests/test_param_check.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: test_param_check_custom_genome_blacklist
-  command: nextflow run main.nf -profile docker,test_fasta_only --only_input true --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz --blacklist ./assets/blacklists/hg38-blacklist.bed -c tests/config/nextflow.config
-  tags:
-    - test_params
-    - params_customgenome
-    - params_customgenome_blacklist
-
-- name: test_param_check_custom_genome_noblacklist
-  command: nextflow run main.nf -profile docker,test_fasta_only --only_input true --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz -c tests/config/nextflow.config
-  tags:
-    - test_params
-    - params_customgenome
-    - params_customgenome_noblacklist
diff --git a/tests/test_peak_callers.yml b/tests/test_peak_callers.yml
deleted file mode 100644
index fcf00f58..00000000
--- a/tests/test_peak_callers.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-- name: test_peak_callers_seacr
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_seacr
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-
-- name: test_peak_callers_macs2
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller macs2 -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_macs2
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed
-
-- name: test_peak_callers_invalid_name
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller test -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_invalid
-  exit_code: 1
-
-- name: test_peak_callers_seacr_macs2
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr,macs2 -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_seacr_macs2
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed
-
-- name: test_peak_callers_macs2_seacr
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller macs2,seacr -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_macs2_seacr
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed
-
-- name: test_peak_callers_seacr_macs2_noigg
-  command: nextflow run main.nf -profile docker,test_no_control --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr,macs2 -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_seacr_macs2_noigg
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed
-
-- name: test_peak_callers_seacr_single_ctrl_multi_rep
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_ctrl_tests
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k4me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k4me3_R2.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R2.seacr.peaks.bed.stringent.bed
-
-- name: test_peak_callers_seacr_multi_single_ctrl_multi_rep
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
-  tags:
-    - test_peak_callers
-    - test_peak_callers_ctrl_tests
-  files:
-    - path: results/03_peak_calling/04_called_peaks/h3k4me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k4me3_R2.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R2.seacr.peaks.bed.stringent.bed
diff --git a/tests/test_verify_output_only_input.yml b/tests/test_verify_output_01_only_input.yml
similarity index 92%
rename from tests/test_verify_output_only_input.yml
rename to tests/test_verify_output_01_only_input.yml
index 31403144..ea6f0d67 100644
--- a/tests/test_verify_output_only_input.yml
+++ b/tests/test_verify_output_01_only_input.yml
@@ -1,7 +1,6 @@
 - name: test_verify_output_only_input
   command: nextflow run main.nf -profile docker,test --only_input true -c tests/config/nextflow.config
   tags:
-    - verify_output
     - verify_output_only_input
   files:
     - path: results/pipeline_info/samplesheet.valid.csv
diff --git a/tests/test_verify_output_save_merged.yml b/tests/test_verify_output_01_save_merged.yml
similarity index 71%
rename from tests/test_verify_output_save_merged.yml
rename to tests/test_verify_output_01_save_merged.yml
index ada48731..d0484570 100644
--- a/tests/test_verify_output_save_merged.yml
+++ b/tests/test_verify_output_01_save_merged.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_save_merged
-  command: nextflow run main.nf -profile docker,test_tech_reps --save_merged_fastq true --only_preqc true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test_tech_reps --save_merged_fastq --only_preqc -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_save
     - verify_output_save_merged
   files:
     - path: results/01_prealign/merged_fastq/h3k27me3_R1_1.merged.fastq.gz
diff --git a/tests/test_verify_output_save_trimmed.yml b/tests/test_verify_output_01_save_trimmed.yml
similarity index 68%
rename from tests/test_verify_output_save_trimmed.yml
rename to tests/test_verify_output_01_save_trimmed.yml
index 43ae6b4a..0e4026d2 100644
--- a/tests/test_verify_output_save_trimmed.yml
+++ b/tests/test_verify_output_01_save_trimmed.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_save_trimmed
-  command: nextflow run main.nf -profile docker,test --only_preqc true --save_trimmed true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_preqc --save_trimmed -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_save
     - verify_output_save_trimmed
   files:
     - path: results/01_prealign/trimgalore/h3k27me3_R1_1.trimmed.fastq.gz
diff --git a/tests/test_verify_output_skip_fastqc.yml b/tests/test_verify_output_01_skip_fastqc.yml
similarity index 83%
rename from tests/test_verify_output_skip_fastqc.yml
rename to tests/test_verify_output_01_skip_fastqc.yml
index 34de90ec..d0eec28a 100644
--- a/tests/test_verify_output_skip_fastqc.yml
+++ b/tests/test_verify_output_01_skip_fastqc.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_skip_fastqc_true
-  command: nextflow run main.nf -profile docker,test --only_preqc true --skip_fastqc true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_preqc --skip_fastqc true -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_skip
     - verify_output_skip_fastqc
     - verify_output_skip_fastqc_true
   files:
@@ -12,9 +10,8 @@
       should_exist: false
 
 - name: test_verify_output_skip_fastqc_false
-  command: nextflow run main.nf -profile docker,test --only_preqc true --skip_fastqc false
+  command: nextflow run main.nf -profile docker,test --only_preqc --skip_fastqc false
   tags:
-    - verify_output
     - verify_output_skip_fastqc
     - verify_output_skip_fastqc_false
   files:
diff --git a/tests/test_verify_output_skip_trimming.yml b/tests/test_verify_output_01_skip_trimming.yml
similarity index 67%
rename from tests/test_verify_output_skip_trimming.yml
rename to tests/test_verify_output_01_skip_trimming.yml
index 489bc339..8cdaf815 100644
--- a/tests/test_verify_output_skip_trimming.yml
+++ b/tests/test_verify_output_01_skip_trimming.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_skip_trimming
-  command: nextflow run main.nf -profile docker,test --only_preqc true --save_trimmed true --skip_trimming true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_preqc --save_trimmed --skip_trimming -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_skip
     - verify_output_skip_trimming
   files:
     - path: results/01_prealign/trimgalore/h3k27me3_R1_1.trimmed.fastq.gz
diff --git a/tests/test_verify_output_save_ref.yml b/tests/test_verify_output_02_save_ref.yml
similarity index 67%
rename from tests/test_verify_output_save_ref.yml
rename to tests/test_verify_output_02_save_ref.yml
index 2d2714a2..b1e95a9e 100644
--- a/tests/test_verify_output_save_ref.yml
+++ b/tests/test_verify_output_02_save_ref.yml
@@ -1,16 +1,10 @@
 - name: test_verify_output_save_ref
   command: nextflow run main.nf -profile docker,test --save_reference true --only_genome true -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_save
     - verify_output_save_ref
   files:
-    - path: results/00_genome/hg38-chr20-genes.bed
-    - path: results/00_genome/hg38-chr20-genes.gtf
-    - path: results/00_genome/hg38-chr20.fa
     - path: results/00_genome/hg38-chr20.fa.fai
     - path: results/00_genome/hg38-chr20.fa.sizes
     - path: results/00_genome/index/hg38-chr20-bowtie2/hg38-chr20.1.bt2
-    - path: results/00_genome/e_coli_U00096_3.fa
     - path: results/00_genome/e_coli_U00096_3.fa.sizes
     - path: results/00_genome/index/e_coli_U00096_3/e_coli_U00096_3.1.bt2
diff --git a/tests/test_verify_output_only_align.yml b/tests/test_verify_output_03_only_align.yml
similarity index 62%
rename from tests/test_verify_output_only_align.yml
rename to tests/test_verify_output_03_only_align.yml
index 097882d9..9e4fd6b3 100644
--- a/tests/test_verify_output_only_align.yml
+++ b/tests/test_verify_output_03_only_align.yml
@@ -1,13 +1,11 @@
 - name: test_verify_output_only_align
-  command: nextflow run main.nf -profile docker,test --only_alignment true --skip_fastqc true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_alignment --skip_fastqc -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_only_align
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.sorted.bam
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.sorted.bam.bai
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam.bai
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.sorted.bam.flagstat
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.sorted.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.flagstat
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.flagstat
diff --git a/tests/test_verify_output_align_intermed.yml b/tests/test_verify_output_03_save_align_intermed.yml
similarity index 77%
rename from tests/test_verify_output_align_intermed.yml
rename to tests/test_verify_output_03_save_align_intermed.yml
index ffae3d87..30cfb1cf 100644
--- a/tests/test_verify_output_align_intermed.yml
+++ b/tests/test_verify_output_03_save_align_intermed.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_align_intermed
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --save_align_intermed true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_filtering --skip_fastqc --skip_preseq --save_align_intermed -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_intermed
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.bam
diff --git a/tests/test_verify_output_save_spikein_align.yml b/tests/test_verify_output_03_save_spikein_align.yml
similarity index 61%
rename from tests/test_verify_output_save_spikein_align.yml
rename to tests/test_verify_output_03_save_spikein_align.yml
index a228d91b..d2144231 100644
--- a/tests/test_verify_output_save_spikein_align.yml
+++ b/tests/test_verify_output_03_save_spikein_align.yml
@@ -1,13 +1,11 @@
 - name: test_verify_output_save_spikein_align
-  command: nextflow run main.nf -profile docker,test --only_alignment true --save_spikein_aligned true --skip_fastqc true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_alignment --save_spikein_aligned --skip_fastqc -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_save_spikein_align
   files:
     - path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.spikein.sorted.bam
     - path: results/02_alignment/bowtie2/spikein/igg_ctrl_R1.spikein.sorted.bam
     - path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.spikein.sorted.bam.bai
     - path: results/02_alignment/bowtie2/spikein/igg_ctrl_R1.spikein.sorted.bam.bai
-    - path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.spikein.sorted.bam.flagstat
-    - path: results/02_alignment/bowtie2/spikein/igg_ctrl_R1.spikein.sorted.bam.flagstat
+    - path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.flagstat
+    - path: results/02_alignment/bowtie2/spikein/igg_ctrl_R1.flagstat
diff --git a/tests/test_verify_output_save_unaligned.yml b/tests/test_verify_output_03_save_unaligned.yml
similarity index 80%
rename from tests/test_verify_output_save_unaligned.yml
rename to tests/test_verify_output_03_save_unaligned.yml
index ca1105ad..ca753098 100644
--- a/tests/test_verify_output_save_unaligned.yml
+++ b/tests/test_verify_output_03_save_unaligned.yml
@@ -1,8 +1,6 @@
 - name: test_verify_output_save_unaligned
-  command: nextflow run main.nf -profile docker,test --only_alignment true --skip_fastqc true --save_unaligned true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_alignment --skip_fastqc --save_unaligned -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_save_unaligned
   files:
     - path: results/02_alignment/bowtie2/target/unmapped/h3k27me3_R1.unmapped_1.fastq.gz
diff --git a/tests/test_verify_output_duplicates.yml b/tests/test_verify_output_04_duplicates.yml
similarity index 60%
rename from tests/test_verify_output_duplicates.yml
rename to tests/test_verify_output_04_duplicates.yml
index d28e9df8..df88932e 100644
--- a/tests/test_verify_output_duplicates.yml
+++ b/tests/test_verify_output_04_duplicates.yml
@@ -1,46 +1,40 @@
 - name: test_verify_output_duplicates_mark
-  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_filtering --skip_fastqc --skip_removeduplicates --skip_preseq -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_duplicates
     - verify_output_align_duplicates_mark
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.bai
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.bai
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.flagstat
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.flagstat
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.flagstat
 
 - name: test_verify_output_duplicates_remove
-  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads false -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_filtering --skip_fastqc --skip_preseq --dedup_target_reads false -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_duplicates
     - verify_output_align_duplicates_remove
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.bai
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam.bai
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.flagstat
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.flagstat
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.flagstat
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.bam
       should_exist: false
 
 - name: test_verify_output_duplicates_remove_target
-  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_filtering --skip_fastqc --skip_preseq --dedup_target_reads true -c tests/config/nextflow.config
   tags:
-    - verify_output
-    - verify_output_align
     - verify_output_align_duplicates
     - verify_output_align_duplicates_remove_target
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.bam
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.bam.bai
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam.bai
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.bam.flagstat
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.dedup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.dedup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.flagstat
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.flagstat
diff --git a/tests/test_verify_output_only_filtering.yml b/tests/test_verify_output_04_only_filtering.yml
similarity index 57%
rename from tests/test_verify_output_only_filtering.yml
rename to tests/test_verify_output_04_only_filtering.yml
index be0032ec..f3a3a024 100644
--- a/tests/test_verify_output_only_filtering.yml
+++ b/tests/test_verify_output_04_only_filtering.yml
@@ -1,12 +1,11 @@
 - name: verify_output_only_filtering
-  command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_filtering --skip_fastqc --skip_removeduplicates --skip_preseq -c tests/config/nextflow.config
   tags:
-    - verify_output
     - verify_output_only_filtering
   files:
     - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.bai
-    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.target.markdup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/h3k27me3_R1.flagstat
     - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.bai
-    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.bam.flagstat
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.target.markdup.sorted.bam.bai
+    - path: results/02_alignment/bowtie2/target/igg_ctrl_R1.flagstat
diff --git a/tests/test_verify_output_only_peak_calling.yml b/tests/test_verify_output_05_only_peak_calling.yml
similarity index 58%
rename from tests/test_verify_output_only_peak_calling.yml
rename to tests/test_verify_output_05_only_peak_calling.yml
index 23bfa767..7de6f567 100644
--- a/tests/test_verify_output_only_peak_calling.yml
+++ b/tests/test_verify_output_05_only_peak_calling.yml
@@ -1,7 +1,6 @@
 - name: test_verify_output_only_peak_calling
-  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling --skip_fastqc --skip_preseq -c tests/config/nextflow.config
   tags:
-    - verify_output
     - verify_output_peak_calling_only_peak_calling
   files:
     - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph
@@ -10,11 +9,8 @@
     - path: results/03_peak_calling/02_clip_bed/igg_ctrl_R1.clipped.bedGraph
     - path: results/03_peak_calling/03_bed_to_bigwig/h3k27me3_R1.bigWig
     - path: results/03_peak_calling/03_bed_to_bigwig/igg_ctrl_R1.bigWig
-    - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
-    - path: results/03_peak_calling/04_called_peaks/igg_ctrl_R1.seacr.peaks.bed.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/h3k27me3_R1.seacr.peaks.stringent.bed
+    - path: results/03_peak_calling/04_called_peaks/seacr/igg_ctrl_R1.seacr.peaks.stringent.bed
       should_exist: false
-    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.bed
-    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.filtered.awk.bed
-    - path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.len.txt
-    - path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.bin500.awk.bed
-    - path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.cut.bed
+    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.awk.bed
+    - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peak_counts.bed
diff --git a/tests/test_verify_output_06_skip_dt_qc.yml b/tests/test_verify_output_06_skip_dt_qc.yml
new file mode 100644
index 00000000..420ea2ad
--- /dev/null
+++ b/tests/test_verify_output_06_skip_dt_qc.yml
@@ -0,0 +1,22 @@
+- name: verify_output_reporting_skip_dtqc_false
+  command: nextflow run main.nf -profile docker,test_full_small --skip_fastqc --skip_multiqc --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_dtqc
+    - verify_output_reporting_skip_dtqc_false
+  files:
+    - path: results/04_reporting/deeptools_qc/all_target_bams.plotCorrelation.pdf
+    - path: results/04_reporting/deeptools_qc/all_target_bams.plotPCA.pdf
+    - path: results/04_reporting/deeptools_qc/h3k4me3_R1.plotFingerprint.pdf
+
+- name: verify_output_reporting_skip_dtqc_true
+  command: nextflow run main.nf -profile docker,test_full_small --skip_fastqc --skip_multiqc --skip_preseq --skip_dt_qc -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_dtqc
+    - verify_output_reporting_skip_dtqc_true
+  files:
+    - path: results/04_reporting/deeptools_qc/all_target_bams.plotCorrelation.pdf
+      should_exist: false
+    - path: results/04_reporting/deeptools_qc/all_target_bams.plotPCA.pdf
+      should_exist: false
+    - path: results/04_reporting/deeptools_qc/h3k4me3_R1.plotFingerprint.pdf
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_heatmaps.yml b/tests/test_verify_output_06_skip_heatmaps.yml
new file mode 100644
index 00000000..216e15f3
--- /dev/null
+++ b/tests/test_verify_output_06_skip_heatmaps.yml
@@ -0,0 +1,19 @@
+- name: verify_output_reporting_skip_heatmaps_false
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_multiqc --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_heatmaps
+    - verify_output_reporting_skip_heatmaps_false
+  files:
+    - path: results/04_reporting/deeptools_heatmaps/gene/h3k27me3_R1.computeMatrix.mat.gz
+    - path: results/04_reporting/deeptools_heatmaps/peaks/h3k27me3_R1.computeMatrix.mat.gz
+
+- name: verify_output_reporting_skip_heatmaps_true
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_multiqc --skip_preseq --skip_heatmaps -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_heatmaps
+    - verify_output_reporting_skip_heatmaps_true
+  files:
+    - path: results/04_reporting/deeptools_heatmaps/gene/h3k27me3_R1.computeMatrix.mat.gz
+      should_exist: false
+    - path: results/04_reporting/deeptools_heatmaps/peaks/h3k27me3_R1.computeMatrix.mat.gz
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_igv.yml b/tests/test_verify_output_06_skip_igv.yml
new file mode 100644
index 00000000..b2b0cc34
--- /dev/null
+++ b/tests/test_verify_output_06_skip_igv.yml
@@ -0,0 +1,16 @@
+- name: verify_output_reporting_skip_igv_false
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_multiqc --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_igv
+    - verify_output_reporting_skip_igv_false
+  files:
+    - path: results/04_reporting/igv/igv_session.xml
+
+- name: verify_output_reporting_skip_igv_true
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_multiqc --skip_preseq --skip_igv -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_igv
+    - verify_output_reporting_skip_igv_true
+  files:
+    - path: results/04_reporting/igv/igv_session.xml
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_multiqc.yml b/tests/test_verify_output_06_skip_multiqc.yml
new file mode 100644
index 00000000..308cae3d
--- /dev/null
+++ b/tests/test_verify_output_06_skip_multiqc.yml
@@ -0,0 +1,16 @@
+- name: verify_output_reporting_skip_multiqc_false
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_multiqc
+    - verify_output_reporting_skip_multiqc_false
+  files:
+    - path: results/04_reporting/multiqc/multiqc_report.html
+
+- name: verify_output_reporting_skip_multiqc_true
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_preseq --skip_multiqc -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_multiqc
+    - verify_output_reporting_skip_multiqc_true
+  files:
+    - path: results/04_reporting/multiqc/multiqc_report.html
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_peak_qc.yml b/tests/test_verify_output_06_skip_peak_qc.yml
new file mode 100644
index 00000000..a7bd0c7d
--- /dev/null
+++ b/tests/test_verify_output_06_skip_peak_qc.yml
@@ -0,0 +1,16 @@
+- name: verify_output_reporting_skip_peak_qc_false
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_peak_qc
+    - verify_output_reporting_skip_peak_qc_false
+  files:
+    - path: results/04_reporting/multiqc/multiqc_data/multiqc_primary_peakcounts_plot.txt
+
+- name: verify_output_reporting_skip_peak_qc_true
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_preseq --skip_peak_qc -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_peak_qc
+    - verify_output_reporting_skip_peak_qc_true
+  files:
+    - path: results/04_reporting/multiqc/multiqc_data/multiqc_primary_peakcounts_plot.txt
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_preseq.yml b/tests/test_verify_output_06_skip_preseq.yml
new file mode 100644
index 00000000..50b2c1e1
--- /dev/null
+++ b/tests/test_verify_output_06_skip_preseq.yml
@@ -0,0 +1,22 @@
+- name: test_verify_output_skip_preseq_false
+  command: nextflow run main.nf -profile docker,test_full_small --skip_fastqc --skip_multiqc --only_filtering -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_preseq
+    - verify_output_reporting_skip_preseq_false
+  files:
+    - path: results/04_reporting/preseq/h3k4me3_R1.command.log
+    - path: results/04_reporting/preseq/h3k4me3_R2.command.log
+    - path: results/04_reporting/preseq/igg_ctrl_R1.command.log
+
+- name: test_verify_output_skip_preseq_true
+  command: nextflow run main.nf -profile docker,test_full_small --skip_fastqc --skip_multiqc --only_filtering --skip_preseq -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_preseq
+    - verify_output_reporting_skip_preseq_true
+  files:
+    - path: results/04_reporting/preseq/h3k4me3_R1.command.log
+      should_exist: false
+    - path: results/04_reporting/preseq/h3k4me3_R2.command.log
+      should_exist: false
+    - path: results/04_reporting/preseq/igg_ctrl_R1.command.log
+      should_exist: false
diff --git a/tests/test_verify_output_06_skip_reporting.yml b/tests/test_verify_output_06_skip_reporting.yml
new file mode 100644
index 00000000..116a33d5
--- /dev/null
+++ b/tests/test_verify_output_06_skip_reporting.yml
@@ -0,0 +1,13 @@
+- name: test_verify_output_skip_reporting
+  command: nextflow run main.nf -profile docker,test --skip_fastqc --skip_reporting -c tests/config/nextflow.config
+  tags:
+    - verify_output_reporting_skip_reporting
+  files:
+    - path: results/04_reporting/igv/igv_session.xml
+      should_exist: false
+    - path: results/04_reporting/deeptools_qc/all_target_bams.plotCorrelation.pdf
+      should_exist: false
+    - path: results/04_reporting/heatmaps/peaks/h3k27me3_R1.plotHeatmap.pdf
+      should_exist: false
+    - path: results/04_reporting/deeptools_heatmaps/gene/h3k4me3_R1.computeMatrix.mat.gz
+      should_exist: false
diff --git a/tests/test_verify_output_skip_frip.yml b/tests/test_verify_output_skip_frip.yml
deleted file mode 100644
index a062f34d..00000000
--- a/tests/test_verify_output_skip_frip.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: test_verify_output_skip_frip_true
-  command: nextflow run main.nf -profile docker,test_full_small --skip_frip true -c tests/config/nextflow.config
-  tags:
-    - verify_output_skip_frip
-  files:
-    - path: results/04_reporting/qc/06_04_frags_in_peaks.csv
-      should_exist: false
-    - path: results/04_reporting/qc/06_04_frags_in_peaks.png
-      should_exist: false
-
-- name: test_verify_output_skip_frip_false
-  command: nextflow run main.nf -profile docker,test_full_small --skip_frip false  -c tests/config/nextflow.config
-  tags:
-    - verify_output_skip_frip
-  files:
-    - path: results/04_reporting/qc/06_04_frags_in_peaks.csv
-    - path: results/04_reporting/qc/06_04_frags_in_peaks.png
diff --git a/tests/test_verify_output_skip_reporting.yml b/tests/test_verify_output_skip_reporting.yml
deleted file mode 100644
index 193dd917..00000000
--- a/tests/test_verify_output_skip_reporting.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-- name: test_verify_output_skip_reporting
-  command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_reporting true -c tests/config/nextflow.config
-  tags:
-    - verify_output
-    - verify_output_reporting
-    - verify_output_reporting_skip_reporting
-  files:
-    - path: results/04_reporting/qc/merged_report.pdf
-      should_exist: false
-    - path: results/04_reporting/multiqc/multiqc_report.html
-      should_exist: false
-    - path: results/04_reporting/heatmaps/peaks/h3k27me3_R1.plotHeatmap.pdf
-      should_exist: false
-    - path: results/04_reporting/igv/igv_session.xml
-      should_exist: false
-
-- name: test_verify_output_skip_reporting_igv
-  command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_igv true -c tests/config/nextflow.config
-  tags:
-    - verify_output
-    - verify_output_reporting
-    - verify_output_reporting_skip_igv
-  files:
-    - path: results/04_reporting/qc/merged_report.pdf
-    - path: results/04_reporting/multiqc/multiqc_report.html
-    - path: results/04_reporting/heatmaps/peaks/h3k27me3_R1.plotHeatmap.pdf
-    - path: results/04_reporting/igv/igv_session.xml
-      should_exist: false
-
-- name: test_verify_output_skip_reporting_heatmaps
-  command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_heatmaps true -c tests/config/nextflow.config
-  tags:
-    - verify_output
-    - verify_output_reporting
-    - verify_output_reporting_skip_heatmaps
-  files:
-    - path: results/04_reporting/qc/merged_report.pdf
-    - path: results/04_reporting/multiqc/multiqc_report.html
-    - path: results/04_reporting/heatmaps/peaks/h3k27me3_R1.plotHeatmap.pdf
-      should_exist: false
-    - path: results/04_reporting/igv/igv_session.xml
-
-- name: test_verify_output_skip_reporting_multiqc
-  command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_multiqc true -c tests/config/nextflow.config
-  tags:
-    - verify_output
-    - verify_output_reporting
-    - verify_output_reporting_skip_multiqc
-  files:
-    - path: results/04_reporting/qc/merged_report.pdf
-    - path: results/04_reporting/multiqc/multiqc_report.html
-      should_exist: false
-    - path: results/04_reporting/heatmaps/peaks/h3k27me3_R1.plotHeatmap.pdf
-    - path: results/04_reporting/igv/igv_session.xml
diff --git a/workflows/cutandrun.nf b/workflows/cutandrun.nf
index b8f7872b..74e7c3f7 100644
--- a/workflows/cutandrun.nf
+++ b/workflows/cutandrun.nf
@@ -27,10 +27,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, "Input sample
 
 ch_blacklist = Channel.empty()
 if (params.blacklist) {
-    ch_blacklist = file(params.blacklist)
+    ch_blacklist = Channel.from( file(params.blacklist) )
 }
 else {
-    ch_blacklist = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)
+    ch_blacklist = Channel.empty()
     WorkflowCutandrun.blacklistWarn(log)
 }
 
@@ -59,7 +59,11 @@ ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIf
 ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
 
 // Header files for MultiQC
-ch_frag_len_header_multiqc = file("$projectDir/assets/multiqc/frag_len_header.txt", checkIfExists: true)
+ch_frag_len_header_multiqc              = file("$projectDir/assets/multiqc/frag_len_header.txt", checkIfExists: true)
+ch_frip_score_header_multiqc            = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
+ch_peak_counts_header_multiqc           = file("$projectDir/assets/multiqc/peak_counts_header.txt", checkIfExists: true)
+ch_peak_counts_consensus_header_multiqc = file("$projectDir/assets/multiqc/peak_counts_consensus_header.txt", checkIfExists: true)
+ch_peak_reprod_header_multiqc           = file("$projectDir/assets/multiqc/peak_reprod_header.txt", checkIfExists: true)
 
 /*
 ========================================================================================
@@ -87,33 +91,27 @@ if ((caller_list + callers).unique().size() != caller_list.size()) {
  * MODULES
  */
 include { INPUT_CHECK                     } from "../subworkflows/local/input_check"
+include { CUT as PEAK_TO_BED              } from '../modules/local/linux/cut'
 include { AWK as AWK_NAME_PEAK_BED        } from "../modules/local/linux/awk"
-include { AWK as AWK_FRAG_BIN             } from "../modules/local/linux/awk"
-include { SAMTOOLS_CUSTOMVIEW             } from "../modules/local/samtools_custom_view"
 include { IGV_SESSION                     } from "../modules/local/python/igv_session"
-include { AWK as AWK_EDIT_PEAK_BED        } from "../modules/local/linux/awk"
-include { CALCULATE_FRIP                  } from "../modules/local/modules/calculate_frip/main"
-include { CUT as CUT_CALC_REPROD          } from "../modules/local/linux/cut"
-include { CALCULATE_PEAK_REPROD           } from "../modules/local/modules/calculate_peak_reprod/main"
-include { EXPORT_META                     } from "../modules/local/export_meta"
-include { EXPORT_META as EXPORT_META_CTRL } from "../modules/local/export_meta"
-include { GENERATE_REPORTS                } from "../modules/local/modules/generate_reports/main"
+include { AWK as AWK_EXTRACT_SUMMITS      } from "../modules/local/linux/awk"
+include { SAMTOOLS_CUSTOMVIEW             } from "../modules/local/samtools_custom_view"
+include { FRAG_LEN_HIST                   } from "../modules/local/python/frag_len_hist"
 include { MULTIQC                         } from "../modules/local/multiqc"
 
 /*
  * SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
  */
-include { PREPARE_GENOME                                 } from "../subworkflows/local/prepare_genome"
-include { FASTQC_TRIMGALORE                              } from "../subworkflows/local/fastqc_trimgalore"
-include { ALIGN_BOWTIE2                                  } from "../subworkflows/local/align_bowtie2"
-include { ANNOTATE_META_AWK as ANNOTATE_BT2_META         } from "../subworkflows/local/annotate_meta_awk"
-include { ANNOTATE_META_AWK as ANNOTATE_BT2_SPIKEIN_META } from "../subworkflows/local/annotate_meta_awk"
-include { ANNOTATE_META_AWK as ANNOTATE_DEDUP_META       } from "../subworkflows/local/annotate_meta_awk"
-include { CONSENSUS_PEAKS                                } from "../subworkflows/local/consensus_peaks"
-include { CONSENSUS_PEAKS as CONSENSUS_PEAKS_ALL         } from "../subworkflows/local/consensus_peaks"
-include { CALCULATE_FRAGMENTS                            } from "../subworkflows/local/calculate_fragments"
-include { ANNOTATE_META_CSV as ANNOTATE_FRIP_META        } from "../subworkflows/local/annotate_meta_csv"
-include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META  } from "../subworkflows/local/annotate_meta_csv"
+include { PREPARE_GENOME                                   } from "../subworkflows/local/prepare_genome"
+include { FASTQC_TRIMGALORE                                } from "../subworkflows/local/fastqc_trimgalore"
+include { ALIGN_BOWTIE2                                    } from "../subworkflows/local/align_bowtie2"
+include { EXTRACT_METADATA_AWK as EXTRACT_BT2_TARGET_META  } from "../subworkflows/local/extract_metadata_awk"
+include { EXTRACT_METADATA_AWK as EXTRACT_BT2_SPIKEIN_META } from "../subworkflows/local/extract_metadata_awk"
+include { EXTRACT_METADATA_AWK as EXTRACT_PICARD_DUP_META  } from "../subworkflows/local/extract_metadata_awk"
+include { CONSENSUS_PEAKS                                  } from "../subworkflows/local/consensus_peaks"
+include { CONSENSUS_PEAKS as CONSENSUS_PEAKS_ALL           } from "../subworkflows/local/consensus_peaks"
+include { EXTRACT_FRAGMENTS                                } from "../subworkflows/local/extract_fragments"
+include { PEAK_QC                                          } from "../subworkflows/local/peak_qc"
 
 /*
 ========================================================================================
@@ -124,25 +122,26 @@ include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META  } from "../subworkflows
 /*
  * MODULES
  */
-include { CAT_FASTQ                                                } from "../modules/nf-core/modules/cat/fastq/main"
-include { SEACR_CALLPEAK                                           } from "../modules/nf-core/modules/seacr/callpeak/main"
-include { SEACR_CALLPEAK as SEACR_CALLPEAK_NOIGG                   } from "../modules/nf-core/modules/seacr/callpeak/main"
-include { MACS2_CALLPEAK                                           } from "../modules/nf-core/modules/macs2/callpeak/main"
-include { MACS2_CALLPEAK as MACS2_CALLPEAK_NOIGG                   } from "../modules/nf-core/modules/macs2/callpeak/main"
-include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE  } from "../modules/nf-core/modules/deeptools/computematrix/main"
-include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/modules/deeptools/computematrix/main"
-include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE      } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
-include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS     } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
-include { BEDTOOLS_INTERSECT                                       } from "../modules/nf-core/modules/bedtools/intersect/main.nf"
-include { CUSTOM_DUMPSOFTWAREVERSIONS                              } from "../modules/local/modules/custom/dumpsoftwareversions/main"
+include { CAT_FASTQ                                                } from "../modules/nf-core/cat/fastq/main"
+include { PRESEQ_LCEXTRAP                                          } from "../modules/local/for_patch/preseq/lcextrap/main"
+include { SEACR_CALLPEAK                                           } from "../modules/nf-core/seacr/callpeak/main"
+include { SEACR_CALLPEAK as SEACR_CALLPEAK_NOIGG                   } from "../modules/nf-core/seacr/callpeak/main"
+include { MACS2_CALLPEAK                                           } from "../modules/nf-core/macs2/callpeak/main"
+include { MACS2_CALLPEAK as MACS2_CALLPEAK_NOIGG                   } from "../modules/nf-core/macs2/callpeak/main"
+include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE  } from "../modules/nf-core/deeptools/computematrix/main"
+include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/deeptools/computematrix/main"
+include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE      } from "../modules/nf-core/deeptools/plotheatmap/main"
+include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS     } from "../modules/nf-core/deeptools/plotheatmap/main"
+include { CUSTOM_DUMPSOFTWAREVERSIONS                              } from "../modules/local/custom_dumpsoftwareversions"
 
 /*
  * SUBWORKFLOW: Consisting entirely of nf-core/modules
  */
 include { MARK_DUPLICATES_PICARD                       } from "../subworkflows/nf-core/mark_duplicates_picard"
 include { MARK_DUPLICATES_PICARD as DEDUPLICATE_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard"
-include { SAMTOOLS_VIEW_SORT_STATS                     } from "../subworkflows/nf-core/samtools_view_sort_stats"
+include { SAMTOOLS_VIEW_SORT_STATS as FILTER_READS     } from "../subworkflows/nf-core/samtools_view_sort_stats"
 include { PREPARE_PEAKCALLING                          } from "../subworkflows/nf-core/prepare_peakcalling"
+include { DEEPTOOLS_QC                                 } from "../subworkflows/nf-core/deeptools_qc"
 
 /*
 ========================================================================================
@@ -154,14 +153,14 @@ workflow CUTANDRUN {
 
     // Init
     ch_software_versions = Channel.empty()
-    ch_frag_len_multiqc  = Channel.empty()
 
     /*
      * SUBWORKFLOW: Uncompress and prepare reference genome files
      */
     if(params.run_genome_prep) {
         PREPARE_GENOME (
-            prepare_tool_indices
+            prepare_tool_indices,
+            ch_blacklist
         )
         ch_software_versions = ch_software_versions.mix(PREPARE_GENOME.out.versions)
     }
@@ -175,19 +174,19 @@ workflow CUTANDRUN {
         )
 
         INPUT_CHECK.out.reads
-            .map {
-                meta, fastq ->
-                    meta.id = meta.id.split("_")[0..-2].join("_")
-                    [ meta, fastq ] }
-            .groupTuple(by: [0])
-            .branch {
-                meta, fastq ->
-                    single  : fastq.size() == 1
-                        return [ meta, fastq.flatten() ]
-                    multiple: fastq.size() > 1
-                        return [ meta, fastq.flatten() ]
-            }
-            .set { ch_fastq }
+        .map {
+            meta, fastq ->
+                meta.id = meta.id.split("_")[0..-2].join("_")
+                [ meta, fastq ] }
+        .groupTuple(by: [0])
+        .branch {
+            meta, fastq ->
+                single  : fastq.size() == 1
+                    return [ meta, fastq.flatten() ]
+                multiple: fastq.size() > 1
+                    return [ meta, fastq.flatten() ]
+        }
+        .set { ch_fastq }
     }
 
     /*
@@ -200,8 +199,8 @@ workflow CUTANDRUN {
         ch_software_versions = ch_software_versions.mix(CAT_FASTQ.out.versions)
 
         CAT_FASTQ.out.reads
-            .mix(ch_fastq.single)
-            .set { ch_cat_fastq }
+        .mix(ch_fastq.single)
+        .set { ch_cat_fastq }
     }
     //EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [READS]]
     //ch_cat_fastq | view
@@ -265,25 +264,66 @@ workflow CUTANDRUN {
         }
     }
     //EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
-    // ch_samtools_bam | view
+    //ch_samtools_bam | view
 
     /*
-     *  SUBWORKFLOW: Filter reads based on quality metrics
-     *  http://biofinysics.blogspot.com/2014/05/how-does-bowtie2-assign-mapq-scores.html
+     * SUBWORKFLOW: extract aligner metadata
      */
-    if (params.run_q_filter) {
-        SAMTOOLS_VIEW_SORT_STATS (
-            ch_samtools_bam
+    ch_metadata_bt2_target  = Channel.empty()
+    ch_metadata_bt2_spikein = Channel.empty()
+    if (params.aligner == "bowtie2" && params.run_alignment) {
+        EXTRACT_BT2_TARGET_META (
+            ch_bowtie2_log,
+            ch_bt2_to_csv_awk,
+            true
         )
-        ch_samtools_bam      = SAMTOOLS_VIEW_SORT_STATS.out.bam
-        ch_samtools_bai      = SAMTOOLS_VIEW_SORT_STATS.out.bai
-        ch_samtools_stats    = SAMTOOLS_VIEW_SORT_STATS.out.stats
-        ch_samtools_flagstat = SAMTOOLS_VIEW_SORT_STATS.out.flagstat
-        ch_samtools_idxstats = SAMTOOLS_VIEW_SORT_STATS.out.idxstats
-        ch_software_versions = ch_software_versions.mix(SAMTOOLS_VIEW_SORT_STATS.out.versions)
+        ch_metadata_bt2_target = EXTRACT_BT2_TARGET_META.out.metadata
+        ch_software_versions   = ch_software_versions.mix(EXTRACT_BT2_TARGET_META.out.versions)
+
+        EXTRACT_BT2_SPIKEIN_META (
+            ch_bowtie2_spikein_log,
+            ch_bt2_to_csv_awk,
+            true
+        )
+        ch_metadata_bt2_spikein = EXTRACT_BT2_SPIKEIN_META.out.metadata
+    }
+    //ch_metadata_bt2_target | view
+    //ch_metadata_bt2_spikein | view
+
+    /*
+     *  SUBWORKFLOW: Filter reads based some standard measures
+     *  - Unmapped reads 0x004
+     *  - Mate unmapped 0x0008
+     *  - Multi-mapped reads
+     *  - Filter out reads aligned to blacklist regions
+     *  - Filter out reads below a threshold q score
+     */ 
+    if (params.run_read_filter) {
+        FILTER_READS (
+            ch_samtools_bam,
+            PREPARE_GENOME.out.allowed_regions.collect{it[1]}.ifEmpty([])
+        )
+        ch_samtools_bam      = FILTER_READS.out.bam
+        ch_samtools_bai      = FILTER_READS.out.bai
+        ch_samtools_stats    = FILTER_READS.out.stats
+        ch_samtools_flagstat = FILTER_READS.out.flagstat
+        ch_samtools_idxstats = FILTER_READS.out.idxstats
+        ch_software_versions = ch_software_versions.mix(FILTER_READS.out.versions)
     }
     //EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
     //ch_samtools_bam | view
+    
+    /*
+     * MODULE: Run preseq on BAM files before de-duplication
+    */
+    ch_preseq_output = Channel.empty()
+    if (params.run_preseq) {
+        PRESEQ_LCEXTRAP (
+            ch_samtools_bam
+        )
+        ch_preseq_output = PRESEQ_LCEXTRAP.out.lc_extrap
+        ch_software_versions = ch_software_versions.mix(PRESEQ_LCEXTRAP.out.versions)
+    }
 
     /*
      * SUBWORKFLOW: Mark duplicates on all samples
@@ -308,7 +348,6 @@ workflow CUTANDRUN {
     /*
      * SUBWORKFLOW: Remove duplicates - default is on IgG controls only
      */
-    ch_dedup_multiqc = Channel.empty()
     if (params.run_remove_dups) {
         DEDUPLICATE_PICARD (
             ch_samtools_bam,
@@ -319,66 +358,35 @@ workflow CUTANDRUN {
         ch_samtools_stats    = DEDUPLICATE_PICARD.out.stats
         ch_samtools_flagstat = DEDUPLICATE_PICARD.out.flagstat
         ch_samtools_idxstats = DEDUPLICATE_PICARD.out.idxstats
-        ch_dedup_multiqc     = DEDUPLICATE_PICARD.out.metrics
         ch_software_versions = ch_software_versions.mix(DEDUPLICATE_PICARD.out.versions)
     }
     //EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
     //ch_samtools_bam | view
 
     /*
-     * SUBWORKFLOW: Annotate meta-data with aligner stats for target and spike-in
-     * the meta-data is annotated additivley so we only need to track the final channel output
-     */
-    if (params.aligner == "bowtie2" && params.run_alignment) {
-        ANNOTATE_BT2_META (
-            ch_samtools_bam,
-            ch_bowtie2_log,
-            ch_bt2_to_csv_awk,
-            "",
-            "_target",
-            true
-        )
-        ch_software_versions = ch_software_versions.mix(ANNOTATE_BT2_META.out.versions)
-
-        ANNOTATE_BT2_SPIKEIN_META (
-            ANNOTATE_BT2_META.out.output,
-            ch_bowtie2_spikein_log,
-            ch_bt2_to_csv_awk,
-            "",
-            "_spikein",
-            true
-        )
-        ch_samtools_bam = ANNOTATE_BT2_SPIKEIN_META.out.output
-    }
-    // META-DATA example state:
-    //[[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false,
-    // bt2_total_reads_spikein:9616, bt2_align1_spikein:1, bt2_align_gt1_spikein:0, bt2_non_aligned_spikein:9615, bt2_total_aligned_spikein:1,
-    // bt2_total_reads_target:9616, bt2_align1_target:315, bt2_align_gt1_target:449, bt2_non_aligned_target:8852, bt2_total_aligned_target:764], BAM]
-    //ch_samtools_bam | view
-    //EXPORT_META ( ch_annotated_meta.collect{ it[0] } )
-
-    /*
-    * SUBWORKFLOW: Annotate meta-data with duplication stats
+    * SUBWORKFLOW: extract duplication stats from picard report
     */
+    ch_metadata_picard_duplicates = Channel.empty()
     if (params.run_mark_dups) {
-        ANNOTATE_DEDUP_META(
-            ch_samtools_bam,
+        EXTRACT_PICARD_DUP_META (
             ch_markduplicates_metrics,
             ch_dummy_file.collect(),
-            "dedup_",
-            "",
             false
         )
-        ch_samtools_bam      = ANNOTATE_DEDUP_META.out.output
-        ch_software_versions = ch_software_versions.mix(ANNOTATE_DEDUP_META.out.versions)
+        ch_metadata_picard_duplicates = EXTRACT_PICARD_DUP_META.out.metadata
+        ch_software_versions          = ch_software_versions.mix(EXTRACT_PICARD_DUP_META.out.versions)
     }
-    //EXAMPLE CHANNEL STRUCT: [[META + dedup_library:unknown library, dedup_unpaired_reads_examined:0, dedup_read_pairs_examined:350, dedup_secondary_or_supplementary_rds:0,
-    // dedup_unmapped_reads:0, dedup_unpaired_read_duplicates:0, dedup_read_pair_duplicates:0, dedup_read_pair_optical_duplicates:0, dedup_percent_duplication:0,
-    // dedup_estimated_library_size:], BAM]
-    //ch_samtools_bam | view
-
-    ch_bedgraph = Channel.empty()
-    ch_bigwig   = Channel.empty()
+    //ch_metadata_picard_duplicates | view
+
+    ch_bedgraph               = Channel.empty()
+    ch_bigwig                 = Channel.empty()
+    ch_seacr_peaks            = Channel.empty()
+    ch_macs2_peaks            = Channel.empty()
+    ch_peaks_primary          = Channel.empty()
+    ch_peaks_secondary        = Channel.empty()
+    ch_peaks_summits          = Channel.empty()
+    ch_consensus_peaks        = Channel.empty()
+    ch_consensus_peaks_unfilt = Channel.empty()
     if(params.run_peak_calling) {
         /*
         * SUBWORKFLOW: Convert BAM files to bedgraph/bigwig and apply configured normalisation strategy
@@ -386,45 +394,50 @@ workflow CUTANDRUN {
         PREPARE_PEAKCALLING(
             ch_samtools_bam,
             ch_samtools_bai,
-            PREPARE_GENOME.out.chrom_sizes,
+            PREPARE_GENOME.out.chrom_sizes.collect(),
             ch_dummy_file,
             params.normalisation_mode,
+            ch_metadata_bt2_spikein
         )
-        ch_samtools_bam      = PREPARE_PEAKCALLING.out.bam
         ch_bedgraph          = PREPARE_PEAKCALLING.out.bedgraph
         ch_bigwig            = PREPARE_PEAKCALLING.out.bigwig
-        ch_software_versions = ch_software_versions.mix(ANNOTATE_DEDUP_META.out.versions)
+        ch_software_versions = ch_software_versions.mix(PREPARE_PEAKCALLING.out.versions)
 
         /*
          * CHANNEL: Separate bedgraphs into target/control
          */
-        ch_bedgraph.branch { it ->
-            target:  it[0].is_control == false
-            control: it[0].is_control == true
-        }
-        .set { ch_bedgraph_split }
-        //ch_bedgraph_split.target | view
-        //ch_bedgraph_split.control | view
+        ch_bedgraph.filter { it -> it[0].is_control == false }
+        .set { ch_bedgraph_target }
+        ch_bedgraph.filter { it -> it[0].is_control == true }
+        .set { ch_bedgraph_control }
+        //ch_bedgraph_target | view
+        //ch_bedgraph_control | view
 
-        ch_seacr_bed = Channel.empty()
-        ch_macs2_bed = Channel.empty()
-        ch_peaks_bed = Channel.empty()
+        /*
+        * CHANNEL: Separate bams into target/control
+        */
+        ch_samtools_bam.filter { it -> it[0].is_control == false }
+        .set { ch_bam_target }
+        ch_samtools_bam.filter { it -> it[0].is_control == true }
+        .set { ch_bam_control }
+        //ch_bam_target | view
+        //ch_bam_control | view
 
         if(params.use_control) {
             /*
-             * MODULE: Call peaks using SEACR with IgG control
-             */
+            * MODULE: Call peaks using SEACR with IgG control
+            */
             if('seacr' in callers) {
                 /*
-                * CHANNEL: Pull control groups
+                * CHANNEL: Subset control groups
                 */
-                ch_bedgraph_split.target.map{
+                ch_bedgraph_target.map{
                     row -> [row[0].control_group, row]
                 }
                 .set { ch_bg_target_ctrlgrp }
                 //ch_bg_target_ctrlgrp | view
 
-                ch_bedgraph_split.control.map{
+                ch_bedgraph_control.map{
                     row -> [row[0].control_group, row]
                 }
                 .set { ch_bg_control_ctrlgrp }
@@ -443,32 +456,25 @@ workflow CUTANDRUN {
 
                 SEACR_CALLPEAK (
                     ch_bedgraph_paired,
-                    params.peak_threshold
+                    params.seacr_peak_threshold
                 )
-                ch_seacr_bed         = SEACR_CALLPEAK.out.bed
+                ch_seacr_peaks       = SEACR_CALLPEAK.out.bed
                 ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
                 // EXAMPLE CHANNEL STRUCT: [[META], BED]
                 //SEACR_CALLPEAK.out.bed | view
             }
 
             if('macs2' in callers) {
-                ch_samtools_bam.branch{ it ->
-                    target:  it[0].is_control == false
-                    control: it[0].is_control == true
-                }
-                .set { ch_samtools_bam_split }
-                // ch_samtools_bam_split.target | view
-
                 /*
-                * CHANNEL: Pull control groups
+                * CHANNEL: Split control groups
                 */
-                ch_samtools_bam_split.target.map{
+                ch_bam_target.map{
                     row -> [row[0].control_group, row]
                 }
                 .set { ch_bam_target_ctrlgrp }
                 //ch_bam_target_ctrlgrp | view
 
-                ch_samtools_bam_split.control.map{
+                ch_bam_control.map{
                     row -> [row[0].control_group, row]
                 }
                 .set { ch_bam_control_ctrlgrp }
@@ -481,7 +487,7 @@ workflow CUTANDRUN {
                 ch_bam_control_ctrlgrp.cross(ch_bam_target_ctrlgrp).map{
                     row -> [row[1][1][0], row[1][1][1], row[0][1][1]]
                 }
-                .set{ch_bam_paired}
+                .set{ ch_bam_paired }
                 // EXAMPLE CHANNEL STRUCT: [[META], TARGET_BAM, CONTROL_BAM]
                 // ch_bam_paired | view
 
@@ -489,10 +495,11 @@ workflow CUTANDRUN {
                     ch_bam_paired,
                     params.macs_gsize
                 )
-                ch_macs2_bed         = MACS2_CALLPEAK.out.bed
+                ch_macs2_peaks       = MACS2_CALLPEAK.out.peak
+                ch_peaks_summits     = MACS2_CALLPEAK.out.bed
                 ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK.out.versions)
                 // EXAMPLE CHANNEL STRUCT: [[META], BED]
-                //MACS2_CALLPEAK.out.bed | view
+                //MACS2_CALLPEAK.out.peak | view
             }
         }
         else {
@@ -503,33 +510,26 @@ workflow CUTANDRUN {
                 /*
                 * CHANNEL: Add fake control channel
                 */
-                ch_bedgraph_split.target.map{ row-> [ row[0], row[1], [] ] }
+                ch_bedgraph_target.map{ row-> [ row[0], row[1], [] ] }
                 .set { ch_bedgraph_target_fctrl }
                 // EXAMPLE CHANNEL STRUCT: [[META], BED, FAKE_CTRL]
                 // ch_bedgraph_target_fctrl | view
 
                 SEACR_CALLPEAK_NOIGG (
                     ch_bedgraph_target_fctrl,
-                    params.peak_threshold
+                    params.seacr_peak_threshold
                 )
-                ch_seacr_bed         = SEACR_CALLPEAK_NOIGG.out.bed
+                ch_seacr_peaks       = SEACR_CALLPEAK_NOIGG.out.bed
                 ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK_NOIGG.out.versions)
                 // EXAMPLE CHANNEL STRUCT: [[META], BED]
                 //SEACR_NO_IGG.out.bed | view
             }
 
             if('macs2' in callers) {
-                ch_samtools_bam.branch{ it ->
-                    target:  it[0].is_control == false
-                    control: it[0].is_control == true
-                }
-                .set { ch_samtools_bam_split }
-                // ch_samtools_bam_split.target | view
-
                 /*
                 * CHANNEL: Add fake control channel
                 */
-                ch_samtools_bam_split.target.map{ row-> [ row[0], row[1], [] ] }
+                ch_bam_target.map{ row-> [ row[0], row[1], [] ] }
                 .set { ch_samtools_bam_target_fctrl }
                 // EXAMPLE CHANNEL STRUCT: [[META], BAM, FAKE_CTRL]
                 //ch_samtools_bam_target_fctrl | view
@@ -538,26 +538,52 @@ workflow CUTANDRUN {
                     ch_samtools_bam_target_fctrl,
                     params.macs_gsize
                 )
-                ch_macs2_bed         = MACS2_CALLPEAK_NOIGG.out.bed
+                ch_macs2_peaks       = MACS2_CALLPEAK_NOIGG.out.peak
+                ch_peaks_summits     = MACS2_CALLPEAK_NOIGG.out.bed
                 ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK_NOIGG.out.versions)
                 // EXAMPLE CHANNEL STRUCT: [[META], BED]
-                // MACS2_CALLPEAK_NOIGG.out.bed | view
+                // MACS2_CALLPEAK_NOIGG.out.peak | view
             }
         }
 
-        // Store output of primary peakcaller in the output channel
+        if ("macs2" in params.callers) {
+            /*
+            * MODULE: Convert narrow or broad peak to bed
+            */
+            PEAK_TO_BED ( ch_macs2_peaks )
+            ch_macs2_peaks       = PEAK_TO_BED.out.file
+            ch_software_versions = ch_software_versions.mix(PEAK_TO_BED.out.versions)
+            // EXAMPLE CHANNEL STRUCT: [[META], BED]
+            //PEAK_TO_BED.out.file | view
+        }
+
+        // Identify the primary peak data stream for downstream analysis
         if(callers[0] == 'seacr') {
-                ch_peaks_bed = ch_seacr_bed
+            ch_peaks_primary   = ch_seacr_peaks
+            ch_peaks_secondary = ch_macs2_peaks
         }
         if(callers[0] == 'macs2') {
-            ch_peaks_bed = ch_macs2_bed
+            ch_peaks_primary   = ch_macs2_peaks
+            ch_peaks_secondary = ch_seacr_peaks
+        }
+
+        if(callers[0] == 'seacr') {
+            /*
+            * MODULE: Extract summits from seacr peak beds
+            */
+            AWK_EXTRACT_SUMMITS (
+                ch_peaks_primary
+            )
+            ch_peaks_summits     = AWK_EXTRACT_SUMMITS.out.file
+            ch_software_versions = ch_software_versions.mix(AWK_EXTRACT_SUMMITS.out.versions)
+            //AWK_EXTRACT_SUMMITS.out.file | view
         }
 
         /*
         * MODULE: Add sample identifier column to peak beds
         */
         AWK_NAME_PEAK_BED (
-            ch_peaks_bed
+            ch_peaks_primary
         )
         ch_software_versions = ch_software_versions.mix(AWK_NAME_PEAK_BED.out.versions)
         // EXAMPLE CHANNEL STRUCT: [[META], BED]
@@ -571,7 +597,7 @@ workflow CUTANDRUN {
             .map { row -> [ 1, row[1] ] }
             .groupTuple(by: [0])
             .map { row ->
-                new_meta = [:]
+                def new_meta = [:]
                 new_meta.put( "id", "all_samples" )
                 [ new_meta, row[1].flatten() ]
             }
@@ -590,32 +616,21 @@ workflow CUTANDRUN {
             * SUBWORKFLOW: Construct group consensus peaks
             */
             CONSENSUS_PEAKS_ALL (
-                ch_peaks_bed_all,
-                params.skip_upset_plots
+                ch_peaks_bed_all
             )
-            ch_software_versions = ch_software_versions.mix(CONSENSUS_PEAKS_ALL.out.versions)
+            ch_consensus_peaks        = CONSENSUS_PEAKS_ALL.out.filtered_bed
+            ch_consensus_peaks_unfilt = CONSENSUS_PEAKS_ALL.out.merged_bed
+            ch_software_versions      = ch_software_versions.mix(CONSENSUS_PEAKS_ALL.out.versions)
             // EXAMPLE CHANNEL STRUCT: [[META], BED]
             //CONSENSUS_PEAKS_ALL.out.bed | view
-
         } else {
             /*
-            * CHANNEL: Group samples based on group
+            * CHANNEL: Group samples based on group name
             */
             AWK_NAME_PEAK_BED.out.file
             .map { row -> [ row[0].group, row[1] ] }
             .groupTuple(by: [0])
-            .map { row ->
-                new_meta = [:]
-                new_meta.put( "id", row[0] )
-                [ new_meta, row[1].flatten() ]
-            }
-            .map { row ->
-                [ row[0], row[1], row[1].size() ]
-            }
-            .filter { row -> row[2] > 1 }
-            .map { row ->
-                [ row[0], row[1] ]
-            }
+            .map { row -> [ [id: row[0]], row[1].flatten() ] }
             .set { ch_peaks_bed_group }
             // EXAMPLE CHANNEL STRUCT: [[id: <GROUP>], [BED1, BED2, BEDn...], count]
             //ch_peaks_bed_group | view
@@ -625,122 +640,55 @@ workflow CUTANDRUN {
             * where there is more than 1 replicate in a group
             */
             CONSENSUS_PEAKS (
-                ch_peaks_bed_group,
-                params.skip_upset_plots
+                ch_peaks_bed_group
             )
-            ch_software_versions = ch_software_versions.mix(CONSENSUS_PEAKS.out.versions)
+            ch_consensus_peaks        = CONSENSUS_PEAKS.out.filtered_bed
+            ch_consensus_peaks_unfilt = CONSENSUS_PEAKS.out.merged_bed
+            ch_software_versions      = ch_software_versions.mix(CONSENSUS_PEAKS.out.versions)
             // EXAMPLE CHANNEL STRUCT: [[META], BED]
             //CONSENSUS_PEAKS.out.bed | view
         }
-
-        /*
-        * SUBWORKFLOW: Calculate fragment bed from bams
-        * - Filter for mapped reads
-        * - Convert to bed file
-        * - Keep the read pairs that are on the same chromosome and fragment length less than 1000bp
-        * - Only extract the fragment related columns using cut
-        */
-        CALCULATE_FRAGMENTS (
-            ch_samtools_bam
-        )
-        ch_software_versions = ch_software_versions.mix(CALCULATE_FRAGMENTS.out.versions)
-        //EXAMPLE CHANNEL STRUCT: NO CHANGE
-        //CALCULATE_FRAGMENTS.out.bed | view
-
-        /*
-        * MODULE: Bin the fragments into 500bp bins ready for downstream reporting
-        */
-        AWK_FRAG_BIN(
-            CALCULATE_FRAGMENTS.out.bed
-        )
-        ch_software_versions = ch_software_versions.mix(AWK_FRAG_BIN.out.versions)
-        //AWK_FRAG_BIN.out.file | view
-
-        /*
-        * CHANNEL: Combine bam and bai files on id
-        */
-        ch_samtools_bam.map { row -> [row[0].id, row ].flatten()}
-        .join ( ch_samtools_bai.map { row -> [row[0].id, row ].flatten()} )
-        .map { row -> [row[1], row[2], row[4]] }
-        .set { ch_bam_bai }
-        // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI]
-        //ch_bam_bai | view
-
-        /*
-        * MODULE: Calculate fragment lengths
-        */
-        SAMTOOLS_CUSTOMVIEW (
-            ch_bam_bai
-        )
-        // ch_software_versions = ch_software_versions.mix(SAMTOOLS_CUSTOMVIEW.out.versions)
-        //SAMTOOLS_CUSTOMVIEW.out.tsv | view
     }
 
+    ch_dt_corrmatrix              = Channel.empty()
+    ch_dt_pcadata                 = Channel.empty()
+    ch_dt_fpmatrix                = Channel.empty()
+    ch_peakqc_frip_mqc            = Channel.empty()
+    ch_peakqc_count_mqc           = Channel.empty()
+    ch_peakqc_count_consensus_mqc = Channel.empty()
+    ch_peakqc_reprod_perc_mqc     = Channel.empty()
+    ch_frag_len_hist_mqc          = Channel.empty()
     if(params.run_reporting) {
         if(params.run_igv) {
             /*
             * MODULE: Create igv session
             */
             IGV_SESSION (
-                PREPARE_GENOME.out.fasta,
-                PREPARE_GENOME.out.gtf,
-                ch_peaks_bed.collect{it[1]}.ifEmpty([]),
+                PREPARE_GENOME.out.fasta.map {it[1]},
+                PREPARE_GENOME.out.fasta_index.map {it[1]},
+                PREPARE_GENOME.out.bed_index,
+                //PREPARE_GENOME.out.gtf.collect(),
+                ch_peaks_primary.collect{it[1]}.filter{ it -> it.size() > 1}.ifEmpty([]),
+                ch_peaks_secondary.collect{it[1]}.filter{ it -> it.size() > 1}.ifEmpty([]),
                 ch_bigwig.collect{it[1]}.ifEmpty([])
             )
             //ch_software_versions = ch_software_versions.mix(IGV_SESSION.out.versions)
         }
 
-        if (params.run_deep_tools && params.run_peak_calling) {
-            /*
-            * MODULE: Extract max signal from peak beds
-            */
-            AWK_EDIT_PEAK_BED (
-                ch_peaks_bed
-            )
-            ch_software_versions = ch_software_versions.mix(AWK_EDIT_PEAK_BED.out.versions)
-            //AWK_EDIT_PEAK_BED.out.file | view
-
-            /*
-            * CHANNEL: Structure output for join on id
-            */
-            AWK_EDIT_PEAK_BED.out.file
-                .map { row -> [row[0].id, row ].flatten()}
-                .set { ch_peaks_bed_id }
-            //ch_peaks_bed_id | view
-
+        if (params.run_deeptools_heatmaps && params.run_peak_calling) {
             /*
             * CHANNEL: Remove IgG from bigwig channel
             */
-            ch_bigwig
-                .filter { it[0].is_control == false }
-                .set { ch_bigwig_no_igg }
+            ch_bigwig.filter { it[0].is_control == false }
+            .set { ch_bigwig_no_igg }
             //ch_bigwig_no_igg | view
 
-            /*
-            * CHANNEL: Join beds and bigwigs on id
-            */
-            ch_bigwig_no_igg
-                .map { row -> [row[0].id, row ].flatten()}
-                .join ( ch_peaks_bed_id )
-                .set { ch_dt_peaks }
-            //ch_dt_peaks | view
-
-            ch_dt_peaks
-                .map { row -> row[1,2] }
-                .set { ch_ordered_bigwig }
-            //ch_ordered_bigwig | view
-
-            ch_dt_peaks
-                .map { row -> row[-1] }
-                .set { ch_ordered_peaks_max }
-            //ch_ordered_peaks_max | view
-
             /*
             * MODULE: Compute DeepTools matrix used in heatmap plotting for Genes
             */
             DEEPTOOLS_COMPUTEMATRIX_GENE (
                 ch_bigwig_no_igg,
-                PREPARE_GENOME.out.bed
+                PREPARE_GENOME.out.bed.collect()
             )
             ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_GENE.out.versions)
 
@@ -752,18 +700,40 @@ workflow CUTANDRUN {
             )
             ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_GENE.out.versions)
 
-            // Run if not empty file size > 1 byte
-            ch_ordered_peaks_max
-                .filter { it -> it.size() > 1}
-                .set { ch_ordered_peaks_max_notempty }
-            //ch_ordered_peaks_max_notempty | view
+            /*
+            * CHANNEL: Structure output for join on id
+            */
+            ch_peaks_summits
+            .map { row -> [row[0].id, row ].flatten()}
+            .set { ch_peaks_summits_id }
+            //ch_peaks_bed_id | view
+
+            /*
+            * CHANNEL: Join beds and bigwigs on id
+            */
+            ch_bigwig_no_igg
+            .map { row -> [row[0].id, row ].flatten()}
+            .join ( ch_peaks_summits_id )
+            .set { ch_dt_bigwig_summits }
+            //ch_dt_peaks | view
+
+            ch_dt_bigwig_summits
+            .map { row -> row[1,2] }
+            .set { ch_ordered_bigwig }
+            //ch_ordered_bigwig | view
+
+            ch_dt_bigwig_summits
+            .map { row -> row[-1] }
+            .filter { it -> it.size() > 1}
+            .set { ch_ordered_peaks_max }
+            //ch_ordered_peaks_max | view
 
             /*
             * MODULE: Compute DeepTools matrix used in heatmap plotting for Peaks
             */
             DEEPTOOLS_COMPUTEMATRIX_PEAKS (
                 ch_ordered_bigwig,
-                ch_ordered_peaks_max_notempty
+                ch_ordered_peaks_max
             )
             ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.versions)
             //EXAMPLE CHANNEL STRUCT: [[META], MATRIX]
@@ -778,166 +748,125 @@ workflow CUTANDRUN {
             ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_PEAKS.out.versions)
         }
 
+        if(params.run_deeptools_qc) {
+            /*
+            * SUBWORKFLOW: Run suite of deeptools QC on bam files
+            */
+            DEEPTOOLS_QC (
+                ch_samtools_bam,
+                ch_samtools_bai
+            )
+            ch_dt_corrmatrix     = DEEPTOOLS_QC.out.correlation_matrix
+            ch_dt_pcadata        = DEEPTOOLS_QC.out.pca_data
+            ch_dt_fpmatrix       = DEEPTOOLS_QC.out.fingerprint_matrix
+            ch_software_versions = ch_software_versions.mix(DEEPTOOLS_QC.out.versions)
+        }
+
         /*
-        * CHANNEL: Join bams and beds on id
+        * CHANNEL: Filter bais for target only
         */
-        ch_samtools_bam
-            .map { row -> [row[0].id, row ].flatten()}
-            .join ( ch_samtools_bai.map { row -> [row[0].id, row ].flatten()} )
-            .join ( ch_peaks_bed.map { row -> [row[0].id, row ].flatten()} )
-            .map { row -> [row[1], row[2], row[4], row[6]] }
-            .set { ch_bam_bai_bed }
-        // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, BED]
-        //ch_bam_bai_bed | view
-
-        ch_samtools_bam_ctrl = ch_samtools_bam
-        if(!params.skip_frip) {
+        ch_samtools_bai.filter { it -> it[0].is_control == false }
+        .set { ch_bai_target }
+        //ch_bai_target | view
+
+        if (params.run_peak_qc && params.run_peak_calling) {
+            /*
+            * CHANNEL: Filter flagstat for target only
+            */
+            ch_samtools_flagstat.filter { it -> it[0].is_control == false }
+            .set { ch_flagstat_target }
+            //ch_flagstat_target | view
+
             /*
-            * MODULE: Calculate Frip scores for samples
+            * SUBWORKFLOW: Extract fragments from bam files for fragment-based FRiP score
             */
-            CALCULATE_FRIP (
-                ch_bam_bai_bed
+            EXTRACT_FRAGMENTS (
+                ch_bam_target
             )
-            ch_software_versions = ch_software_versions.mix(CALCULATE_FRIP.out.versions)
 
             /*
-            * SUBWORKFLOW: Annotate meta-data with frip stats
+            * SUBWORKFLOW: Run suite of peak QC on peaks
             */
-            ANNOTATE_FRIP_META (
-                ch_samtools_bam,
-                CALCULATE_FRIP.out.frips,
-                "",
-                ""
+            PEAK_QC(
+                ch_peaks_primary,
+                AWK_NAME_PEAK_BED.out.file,
+                ch_consensus_peaks,
+                ch_consensus_peaks_unfilt,
+                EXTRACT_FRAGMENTS.out.bed,
+                ch_flagstat_target,
+                params.min_frip_overlap,
+                ch_frip_score_header_multiqc,
+                ch_peak_counts_header_multiqc,
+                ch_peak_counts_consensus_header_multiqc,
+                ch_peak_reprod_header_multiqc
             )
-            ch_samtools_bam = ANNOTATE_FRIP_META.out.output
-            //ch_samtools_bam | view
+            ch_peakqc_frip_mqc             = PEAK_QC.out.primary_frip_mqc
+            ch_peakqc_count_mqc            = PEAK_QC.out.primary_count_mqc
+            ch_peakqc_count_consensus_mqc  = PEAK_QC.out.consensus_count_mqc
+            ch_peakqc_reprod_perc_mqc      = PEAK_QC.out.reprod_perc_mqc
+            ch_software_versions           = ch_software_versions.mix(PEAK_QC.out.versions)
         }
-       
-        /*
-        * MODULE: Trim unwanted columns for downstream reporting
-        */
-        CUT_CALC_REPROD (
-            AWK_NAME_PEAK_BED.out.file
-        )
-        ch_software_versions = ch_software_versions.mix(CUT_CALC_REPROD.out.versions)
+        //ch_peakqc_reprod_perc_mqc | view
 
         /*
-        * CHANNEL: Group samples based on group
-        */
-        CUT_CALC_REPROD.out.file
-            .map { row -> [ row[0].group, row[1] ] }
-            .groupTuple(by: [0])
-            .map { row ->
-                new_meta = [:]
-                new_meta.put( "id", row[0] )
-                [ new_meta, row[1].flatten() ]
-            }
-            .map { row ->
-                [ row[0], row[1], row[1].size() ]
-            }
-            .filter { row -> row[2] > 1 }
-            .map { row ->
-                [ row[0], row[1] ]
-            }
-        .set { ch_seacr_bed_group_2 }
-
-        /*
-        * CHANNEL: Per group, create a channel per one against all combination
+        * CHANNEL: Combine bam and bai files on id
         */
-        ch_seacr_bed_group_2
-            .flatMap{
-                row ->
-                new_output = []
-                row[1].each{ file ->
-                    files_copy = row[1].collect()
-                    files_copy.remove(files_copy.indexOf(file))
-                    new_output.add([[id: file.name.split("\\.")[0]], file, files_copy])
-                }
-                new_output
-            }
-        .set { ch_beds_intersect }
-        //EXAMPLE CHANNEL STRUCT: [[META], BED (-a), [BED...n] (-b)]
-        //ch_beds_intersect | view
+        ch_bam_target.map { row -> [row[0].id, row ].flatten()}
+        .join ( ch_bai_target.map { row -> [row[0].id, row ].flatten()} )
+        .map { row -> [row[1], row[2], row[4]] }
+        .set { ch_bam_bai }
+        // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI]
+        //ch_bam_bai | view
 
         /*
-        * MODULE: Find intra-group overlap
+        * MODULE: Calculate fragment lengths
         */
-        BEDTOOLS_INTERSECT (
-            ch_beds_intersect,
-            "bed"
+        SAMTOOLS_CUSTOMVIEW (
+            ch_bam_bai
         )
-        ch_software_versions = ch_software_versions.mix(BEDTOOLS_INTERSECT.out.versions)
-        //EXAMPLE CHANNEL STRUCT: [[META], BED]
-        //BEDTOOLS_INTERSECT.out.intersect | view
+        ch_software_versions = ch_software_versions.mix(SAMTOOLS_CUSTOMVIEW.out.versions)
+        //SAMTOOLS_CUSTOMVIEW.out.tsv | view
 
         /*
-        * MODULE: Use overlap to calculate a peak repro %
+        * CHANNEL: Prepare data for generate reports
         */
-        CALCULATE_PEAK_REPROD (
-            BEDTOOLS_INTERSECT.out.intersect
-        )
-        ch_software_versions = ch_software_versions.mix(CALCULATE_PEAK_REPROD.out.versions)
-        //EXAMPLE CHANNEL STRUCT: [[META], CSV]
-        //CALCULATE_PEAK_REPROD.out.csv
+        // Make sure files are always in order for resume
+        ch_frag_len = SAMTOOLS_CUSTOMVIEW.out.tsv
+        .toSortedList { row -> row[0].id }
+        .map {
+            list ->
+            def output = []
+            list.each{ v -> output.add(v[1]) }
+            output
+        }
+        //ch_frag_len | view
 
         /*
-        * SUBWORKFLOW: Annotate meta-data with peak stats
+        * MODULE: Calculate fragment length histogram for mqc
         */
-        ANNOTATE_PEAK_REPRO_META (
-            ch_samtools_bam,
-            CALCULATE_PEAK_REPROD.out.csv,
-            "",
-            ""
+        FRAG_LEN_HIST(
+            ch_frag_len,
+            ch_frag_len_header_multiqc
         )
-        ch_samtools_bam = ANNOTATE_PEAK_REPRO_META.out.output
-        //ch_samtools_bam | view
-        //ANNOTATE_PEAK_REPRO_META.out.output | view
+        ch_frag_len_hist_mqc = FRAG_LEN_HIST.out.frag_len_mqc
+        ch_software_versions = ch_software_versions.mix(FRAG_LEN_HIST.out.versions)
+    }
+    //ch_frag_len_hist_mqc | view
 
-        /*
-        * MODULE: Export meta-data to csv file
-        */
-        EXPORT_META (
-            ch_samtools_bam.collect{it[0]},
-            "meta_table"
-        )
+    if (params.run_multiqc) {
+        workflow_summary    = WorkflowCutandrun.paramsSummaryMultiqc(workflow, summary_params)
+        ch_workflow_summary = Channel.value(workflow_summary)
 
         /*
-        * MODULE: Export meta-data to csv file
+        * MODULE: Collect software versions used in pipeline
         */
-        EXPORT_META_CTRL (
-            ch_samtools_bam_ctrl.collect{it[0]},
-            "meta_table_ctrl"
+        CUSTOM_DUMPSOFTWAREVERSIONS (
+            ch_software_versions.unique().collectFile()
         )
 
         /*
-        * MODULE: Generate python reporting using mixture of meta-data and direct file processing
+        * MODULE: Multiqc
         */
-        GENERATE_REPORTS(
-            EXPORT_META.out.csv.collect().ifEmpty([]),  // meta-data report stats
-            EXPORT_META_CTRL.out.csv,                   // meta-data report stats
-            SAMTOOLS_CUSTOMVIEW.out.tsv.collect{it[1]}, // raw fragments
-            AWK_FRAG_BIN.out.file.collect{it[1]},       // binned fragments
-            ch_peaks_bed.collect{it[1]},                // peak beds
-            ch_frag_len_header_multiqc                  // multiqc config header for fragment length distribution plot
-        )
-        ch_frag_len_multiqc  = GENERATE_REPORTS.out.frag_len_multiqc
-        ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.versions)
-    }
-
-    /*
-    * MODULE: Collect software versions used in pipeline
-    */
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_software_versions.unique().collectFile()
-    )
-
-    /*
-     * MODULE: Multiqc
-     */
-    if (params.run_multiqc) {
-        workflow_summary    = WorkflowCutandrun.paramsSummaryMultiqc(workflow, summary_params)
-        ch_workflow_summary = Channel.value(workflow_summary)
-
         MULTIQC (
             ch_multiqc_config,
             ch_multiqc_custom_config.collect().ifEmpty([]),
@@ -953,7 +882,15 @@ workflow CUTANDRUN {
             ch_samtools_flagstat.collect{it[1]}.ifEmpty([]),
             ch_samtools_idxstats.collect{it[1]}.ifEmpty([]),
             ch_markduplicates_metrics.collect{it[1]}.ifEmpty([]),
-            ch_frag_len_multiqc.collect().ifEmpty([])
+            ch_preseq_output.collect{it[1]}.ifEmpty([]),
+            ch_dt_corrmatrix.collect{it[1]}.ifEmpty([]),
+            ch_dt_pcadata.collect{it[1]}.ifEmpty([]),
+            ch_dt_fpmatrix.collect{it[1]}.ifEmpty([]),
+            ch_peakqc_count_mqc.collect{it[1]}.ifEmpty([]),
+            ch_peakqc_frip_mqc.collect{it[1]}.ifEmpty([]),
+            ch_peakqc_count_consensus_mqc.collect{it[1]}.ifEmpty([]),
+            ch_peakqc_reprod_perc_mqc.collect().ifEmpty([]),
+            ch_frag_len_hist_mqc.collect().ifEmpty([])
         )
         multiqc_report = MULTIQC.out.report.toList()
     }
@@ -966,6 +903,9 @@ workflow CUTANDRUN {
 workflow.onComplete {
     NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     NfcoreTemplate.summary(workflow, params, log)
+    if (params.hook_url) {
+        NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log)
+    }
 }
 
 ////////////////////////////////////////////////////