diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..ea27a58
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}
diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..b6b3190
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..7a2dabc
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,4 @@
+*.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
new file mode 100644
index 0000000..191fabd
--- /dev/null
+++ b/.github/.dockstore.yml
@@ -0,0 +1,6 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config
+    publish: True
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 0000000..048c967
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,118 @@
+# nf-core/createpanelrefs: Contributing Guidelines
+
+Hi there!
+Many thanks for taking an interest in improving nf-core/createpanelrefs.
+
+We try to manage the required tasks for nf-core/createpanelrefs using GitHub issues, you probably came to this page when creating one.
+Please use the pre-filled template to save time.
+
+However, don't be put off by this template - other more general issues and suggestions are welcome!
+Contributions to the code are even more welcome ;)
+
+> If you need help using or modifying nf-core/createpanelrefs then the best place to ask is on the nf-core Slack [#createpanelrefs](https://nfcore.slack.com/channels/createpanelrefs) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Contribution workflow
+
+If you'd like to write some code for nf-core/createpanelrefs, the standard workflow is as follows:
+
+1. Check that there isn't already an issue about your idea in the [nf-core/createpanelrefs issues](https://github.com/nf-core/createpanelrefs/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/createpanelrefs repository](https://github.com/nf-core/createpanelrefs) to your GitHub account
+3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
+4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+
+If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
+
+## Tests
+
+When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
+Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
+
+There are typically two types of tests that run:
+
+### Lint tests
+
+`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+
+If any failures or warnings are encountered, please follow the listed URL for more documentation.
+
+### Pipeline tests
+
+Each `nf-core` pipeline should be set up with a minimal set of test-data.
+`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
+If there are any failures then the automated tests fail.
+These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+
+## Patch
+
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
+
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
+
+## Getting help
+
+For further information/help, please consult the [nf-core/createpanelrefs documentation](https://nf-co.re/createpanelrefs/usage) and don't hesitate to get in touch on the nf-core Slack [#createpanelrefs](https://nfcore.slack.com/channels/createpanelrefs) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## Pipeline contribution conventions
+
+To make the nf-core/createpanelrefs code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+
+### Adding a new step
+
+If you wish to contribute a new step, please use the following coding standards:
+
+1. Define the corresponding input channel into your new process from the expected previous process channel
+2. Write the process block (see below).
+3. Define the output channel if needed (see below).
+4. Add any new parameters to `nextflow.config` with a default (see below).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+6. Add sanity checks and validation for all relevant parameters.
+7. Perform local tests to validate that the new code works as expected.
+8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+
+### Default values
+
+Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+
+Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+
+### Default processes resource requirements
+
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+
+### Naming schemes
+
+Please use the following naming schemes, to make it easy to understand what is going where.
+
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+
+### Nextflow version bumping
+
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+
+### Images and figures
+
+For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/createpanelrefs/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 0000000..3519546
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,50 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/createpanelrefs pipeline documentation](https://nf-co.re/createpanelrefs/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/createpanelrefs _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..50f9ba4
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #createpanelrefs channel"
+    url: https://nfcore.slack.com/channels/createpanelrefs
+    about: Discussion about the nf-core/createpanelrefs pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 0000000..b4f4605
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/createpanelrefs pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..44f4971
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,25 @@
+<!--
+# nf-core/createpanelrefs pull request
+
+Many thanks for contributing to nf-core/createpanelrefs!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/createpanelrefs/tree/master/.github/CONTRIBUTING.md)
+-->
+
+## PR checklist
+
+- [ ] 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/createpanelrefs/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/createpanelrefs _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.
+- [ ] Output Documentation in `docs/output.md` is updated.
+- [ ] `CHANGELOG.md` is updated.
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
new file mode 100644
index 0000000..57f3573
--- /dev/null
+++ b/.github/workflows/awsfulltest.yml
@@ -0,0 +1,39 @@
+name: nf-core AWS full size tests
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/createpanelrefs'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        # 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 }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/createpanelrefs/work-${{ github.sha }}
+          parameters: |
+            {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/createpanelrefs/results-${{ github.sha }}"
+            }
+          profiles: test_full
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
new file mode 100644
index 0000000..1c7cf00
--- /dev/null
+++ b/.github/workflows/awstest.yml
@@ -0,0 +1,33 @@
+name: nf-core AWS test
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/createpanelrefs'
+    runs-on: ubuntu-latest
+    steps:
+      # Launch workflow using Tower CLI tool action
+      - name: Launch workflow via tower
+        uses: seqeralabs/action-tower-launch@v2
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/createpanelrefs/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/createpanelrefs/results-test-${{ github.sha }}"
+            }
+          profiles: test
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
new file mode 100644
index 0000000..88ba082
--- /dev/null
+++ b/.github/workflows/branch.yml
@@ -0,0 +1,44 @@
+name: nf-core branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+on:
+  pull_request_target:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      - name: Check PRs
+        if: github.repository == 'nf-core/createpanelrefs'
+        run: |
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/createpanelrefs ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## This PR is against the `master` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
+            The `master` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+
+            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+            Note that even after this, the test will continue to show as failing until you push a new commit.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..4ca7478
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,43 @@
+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+env:
+  NXF_ANSI_LOG: false
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/createpanelrefs') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Run pipeline with test data
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
new file mode 100644
index 0000000..694e90e
--- /dev/null
+++ b/.github/workflows/clean-up.yml
@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
new file mode 100644
index 0000000..de2eba2
--- /dev/null
+++ b/.github/workflows/fix-linting.yml
@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/createpanelrefs'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "result=pass" >> $GITHUB_OUTPUT
+          else
+            echo "result=fail" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
new file mode 100644
index 0000000..888cb4b
--- /dev/null
+++ b/.github/workflows/linting.yml
@@ -0,0 +1,108 @@
+name: nf-core linting
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
+
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+          architecture: "x64"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core
+
+      - name: Run nf-core lint
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: linting-logs
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
new file mode 100644
index 0000000..0bbcd30
--- /dev/null
+++ b/.github/workflows/linting_comment.yml
@@ -0,0 +1,28 @@
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+          workflow_conclusion: completed
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5124c9a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
diff --git a/.gitpod.yml b/.gitpod.yml
new file mode 100644
index 0000000..25488dc
--- /dev/null
+++ b/.gitpod.yml
@@ -0,0 +1,19 @@
+image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
diff --git a/.nf-core.yml b/.nf-core.yml
new file mode 100644
index 0000000..3805dc8
--- /dev/null
+++ b/.nf-core.yml
@@ -0,0 +1 @@
+repository_type: pipeline
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..0c31cdb
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..437d763
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,12 @@
+email_template.html
+adaptivecard.json
+slackreport.json
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+bin/
diff --git a/.prettierrc.yml b/.prettierrc.yml
new file mode 100644
index 0000000..c81f9a7
--- /dev/null
+++ b/.prettierrc.yml
@@ -0,0 +1 @@
+printWidth: 120
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..92e5780
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,16 @@
+# nf-core/createpanelrefs: Changelog
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## v1.0dev - [date]
+
+Initial release of nf-core/createpanelrefs, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
diff --git a/CITATIONS.md b/CITATIONS.md
new file mode 100644
index 0000000..9b55cf7
--- /dev/null
+++ b/CITATIONS.md
@@ -0,0 +1,41 @@
+# nf-core/createpanelrefs: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
+  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+
+## Software packaging/containerisation tools
+
+- [Anaconda](https://anaconda.com)
+
+  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+
+  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+
+  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
+- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
+  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 0000000..f4fd052
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,111 @@
+# Code of Conduct at nf-core (v1.0)
+
+## Our Pledge
+
+In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
+
+- Age
+- Body size
+- Familial status
+- Gender identity and expression
+- Geographical location
+- Level of experience
+- Nationality and national origins
+- Native language
+- Physical and neurological ability
+- Race or ethnicity
+- Religion
+- Sexual identity and orientation
+- Socioeconomic status
+
+Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance.
+
+## Preamble
+
+> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply.
+
+An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva.
+
+nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
+
+We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc.
+
+Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
+
+We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
+
+Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re
+
+## Our Responsibilities
+
+The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
+
+The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
+
+## When are where does this Code of Conduct apply?
+
+Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference:
+
+- Communicating with an official project email address.
+- Communicating with community members within the nf-core Slack channel.
+- Participating in hackathons organised by nf-core (both online and in-person events).
+- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence.
+- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc.
+- Representing nf-core on social media. This includes both official and personal accounts.
+
+## nf-core cares 😊
+
+nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order):
+
+- Ask for consent before sharing another community member’s personal information (including photographs) on social media.
+- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity.
+- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
+- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.)
+- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can)
+- Focus on what is best for the team and the community. (When in doubt, ask)
+- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn.
+- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!)
+- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**)
+- Take breaks when you feel like you need them.
+- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.)
+
+## nf-core frowns on 😕
+
+The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces.
+
+- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom.
+- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online.
+- Spamming or trolling of individuals on social media.
+- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention.
+- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience.
+
+### Online Trolling
+
+The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately.
+
+All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls.
+
+## Procedures for Reporting CoC violations
+
+If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible.
+
+You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s).
+
+Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course.
+
+All reports will be handled with utmost discretion and confidentially.
+
+## Attribution and Acknowledgements
+
+- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4)
+- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition)
+- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/)
+- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla)
+
+## Changelog
+
+### v1.0 - March 12th, 2021
+
+- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC.
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..897f9b7
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) @maxulysse
+
+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.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..e053d15
--- /dev/null
+++ b/README.md
@@ -0,0 +1,106 @@
+# ![nf-core/createpanelrefs](docs/images/nf-core-createpanelrefs_logo_light.png#gh-light-mode-only) ![nf-core/createpanelrefs](docs/images/nf-core-createpanelrefs_logo_dark.png#gh-dark-mode-only)
+
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/createpanelrefs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![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/createpanelrefs)
+
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23createpanelrefs-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/createpanelrefs)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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
+
+**nf-core/createpanelrefs** is a bioinformatics pipeline that ...
+
+<!-- TODO nf-core:
+   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
+   major pipeline sections and the types of output it produces. You're giving an overview to someone new
+   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
+-->
+
+<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
+## Usage
+
+> **Note**
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+> with `-profile test` before running the workflow on actual data.
+
+<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
+     Explain what rows and columns represent. For instance (please edit as appropriate):
+
+First, prepare a samplesheet with your input data that looks as follows:
+
+`samplesheet.csv`:
+
+```csv
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+```
+
+Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+
+-->
+
+Now, you can run the pipeline using:
+
+<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+
+```bash
+nextflow run nf-core/createpanelrefs \
+   -profile <docker/singularity/.../institute> \
+   --input samplesheet.csv \
+   --outdir <OUTDIR>
+```
+
+> **Warning:**
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/createpanelrefs/usage) and the [parameter documentation](https://nf-co.re/createpanelrefs/parameters).
+
+## Pipeline output
+
+To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/createpanelrefs/results) tab on the nf-core website pipeline page.
+For more details about the output files and reports, please refer to the
+[output documentation](https://nf-co.re/createpanelrefs/output).
+
+## Credits
+
+nf-core/createpanelrefs was originally written by @maxulysse.
+
+We thank the following people for their extensive assistance in the development of this pipeline:
+
+<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+
+For further information or help, don't hesitate to get in touch on the [Slack `#createpanelrefs` channel](https://nfcore.slack.com/channels/createpanelrefs) (you can join with [this invite](https://nf-co.re/join/slack)).
+
+## Citations
+
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
+<!-- If you use  nf-core/createpanelrefs for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
+You can cite the `nf-core` publication as follows:
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
new file mode 100644
index 0000000..b62675b
--- /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/createpanelrefs 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/email_template.html b/assets/email_template.html
new file mode 100644
index 0000000..91e6caf
--- /dev/null
+++ b/assets/email_template.html
@@ -0,0 +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">
+
+  <meta name="description" content="nf-core/createpanelrefs: Generate Panel of Normals, models or other similar references from lots of samples">
+  <title>nf-core/createpanelrefs 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">
+
+<h1>nf-core/createpanelrefs v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/createpanelrefs execution completed unsuccessfully!</h4>
+        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+        <p>The full error message was:</p>
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+    </div>
+    """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        nf-core/createpanelrefs execution completed successfully!
+    </div>
+    """
+}
+%>
+
+<p>The workflow was completed at <strong>$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>
+
+<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/createpanelrefs</p>
+<p><a href="https://github.com/nf-core/createpanelrefs">https://github.com/nf-core/createpanelrefs</a></p>
+
+</div>
+
+</body>
+</html>
diff --git a/assets/email_template.txt b/assets/email_template.txt
new file mode 100644
index 0000000..2e2bb77
--- /dev/null
+++ b/assets/email_template.txt
@@ -0,0 +1,39 @@
+----------------------------------------------------
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
+  nf-core/createpanelrefs v${version}
+----------------------------------------------------
+Run Name: $runName
+
+<% if (success){
+    out << "## nf-core/createpanelrefs execution completed successfully! ##"
+} else {
+    out << """####################################################
+## nf-core/createpanelrefs execution completed unsuccessfully! ##
+####################################################
+The exit status of the task that caused the workflow execution to fail was: $exitStatus.
+The full error message was:
+
+${errorReport}
+"""
+} %>
+
+
+The workflow was completed at $dateComplete (duration: $duration)
+
+The command used to launch the workflow was as follows:
+
+  $commandLine
+
+
+
+Pipeline Configuration:
+-----------------------
+<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
+
+--
+nf-core/createpanelrefs
+https://github.com/nf-core/createpanelrefs
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
new file mode 100644
index 0000000..84155f8
--- /dev/null
+++ b/assets/methods_description_template.yml
@@ -0,0 +1,29 @@
+id: "nf-core-createpanelrefs-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "nf-core/createpanelrefs Methods Description"
+section_href: "https://github.com/nf-core/createpanelrefs"
+plot_type: "html"
+## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
+## You inject any metadata in the Nextflow '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using nf-core/createpanelrefs v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>The pipeline was executed with Nextflow v${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>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
+  <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. doi: <a href="https://doi.org/10.1038/nbt.3820">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. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
new file mode 100644
index 0000000..c7acb61
--- /dev/null
+++ b/assets/multiqc_config.yml
@@ -0,0 +1,13 @@
+report_comment: >
+  This report has been generated by the <a href="https://github.com/nf-core/createpanelrefs/1.0dev" target="_blank">nf-core/createpanelrefs</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/createpanelrefs/1.0dev/output" target="_blank">documentation</a>.
+report_section_order:
+  "nf-core-createpanelrefs-methods-description":
+    order: -1000
+  software_versions:
+    order: -1001
+  "nf-core-createpanelrefs-summary":
+    order: -1002
+
+export_plots: true
diff --git a/assets/nf-core-createpanelrefs_logo_light.png b/assets/nf-core-createpanelrefs_logo_light.png
new file mode 100644
index 0000000..e73f972
Binary files /dev/null and b/assets/nf-core-createpanelrefs_logo_light.png differ
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
new file mode 100644
index 0000000..5f653ab
--- /dev/null
+++ b/assets/samplesheet.csv
@@ -0,0 +1,3 @@
+sample,fastq_1,fastq_2
+SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
+SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
diff --git a/assets/schema_input.json b/assets/schema_input.json
new file mode 100644
index 0000000..95a560d
--- /dev/null
+++ b/assets/schema_input.json
@@ -0,0 +1,36 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/createpanelrefs/master/assets/schema_input.json",
+    "title": "nf-core/createpanelrefs pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample name must be provided and cannot contain spaces"
+            },
+            "fastq_1": {
+                "type": "string",
+                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "fastq_2": {
+                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
+                "anyOf": [
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ]
+            }
+        },
+        "required": ["sample", "fastq_1"]
+    }
+}
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
new file mode 100644
index 0000000..d3baaf5
--- /dev/null
+++ b/assets/sendmail_template.txt
@@ -0,0 +1,53 @@
+To: $email
+Subject: $subject
+Mime-Version: 1.0
+Content-Type: multipart/related;boundary="nfcoremimeboundary"
+
+--nfcoremimeboundary
+Content-Type: text/html; charset=utf-8
+
+$email_html
+
+--nfcoremimeboundary
+Content-Type: image/png;name="nf-core-createpanelrefs_logo.png"
+Content-Transfer-Encoding: base64
+Content-ID: <nfcorepipelinelogo>
+Content-Disposition: inline; filename="nf-core-createpanelrefs_logo_light.png"
+
+<% out << new File("$projectDir/assets/nf-core-createpanelrefs_logo_light.png").
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' ) %>
+
+<%
+if (mqcFile){
+def mqcFileObj = new File("$mqcFile")
+if (mqcFileObj.length() < mqcMaxSize){
+out << """
+--nfcoremimeboundary
+Content-Type: text/html; name=\"multiqc_report\"
+Content-Transfer-Encoding: base64
+Content-ID: <mqcreport>
+Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
+
+${mqcFileObj.
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' )}
+"""
+}}
+%>
+
+--nfcoremimeboundary--
diff --git a/assets/slackreport.json b/assets/slackreport.json
new file mode 100644
index 0000000..663bd09
--- /dev/null
+++ b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "nf-core/createpanelrefs v${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
new file mode 100755
index 0000000..4a758fe
--- /dev/null
+++ b/bin/check_samplesheet.py
@@ -0,0 +1,259 @@
+#!/usr/bin/env python
+
+
+"""Provide a command line tool to validate and transform tabular samplesheets."""
+
+
+import argparse
+import csv
+import logging
+import sys
+from collections import Counter
+from pathlib import Path
+
+logger = logging.getLogger()
+
+
+class RowChecker:
+    """
+    Define a service that can validate and transform each given row.
+
+    Attributes:
+        modified (list): A list of dicts, where each dict corresponds to a previously
+            validated and transformed row. The order of rows is maintained.
+
+    """
+
+    VALID_FORMATS = (
+        ".fq.gz",
+        ".fastq.gz",
+    )
+
+    def __init__(
+        self,
+        sample_col="sample",
+        first_col="fastq_1",
+        second_col="fastq_2",
+        single_col="single_end",
+        **kwargs,
+    ):
+        """
+        Initialize the row checker with the expected column names.
+
+        Args:
+            sample_col (str): The name of the column that contains the sample name
+                (default "sample").
+            first_col (str): The name of the column that contains the first (or only)
+                FASTQ file path (default "fastq_1").
+            second_col (str): The name of the column that contains the second (if any)
+                FASTQ file path (default "fastq_2").
+            single_col (str): The name of the new column that will be inserted and
+                records whether the sample contains single- or paired-end sequencing
+                reads (default "single_end").
+
+        """
+        super().__init__(**kwargs)
+        self._sample_col = sample_col
+        self._first_col = first_col
+        self._second_col = second_col
+        self._single_col = single_col
+        self._seen = set()
+        self.modified = []
+
+    def validate_and_transform(self, row):
+        """
+        Perform all validations on the given row and insert the read pairing status.
+
+        Args:
+            row (dict): A mapping from column headers (keys) to elements of that row
+                (values).
+
+        """
+        self._validate_sample(row)
+        self._validate_first(row)
+        self._validate_second(row)
+        self._validate_pair(row)
+        self._seen.add((row[self._sample_col], row[self._first_col]))
+        self.modified.append(row)
+
+    def _validate_sample(self, row):
+        """Assert that the sample name exists and convert spaces to underscores."""
+        if len(row[self._sample_col]) <= 0:
+            raise AssertionError("Sample input is required.")
+        # Sanitize samples slightly.
+        row[self._sample_col] = row[self._sample_col].replace(" ", "_")
+
+    def _validate_first(self, row):
+        """Assert that the first FASTQ entry is non-empty and has the right format."""
+        if len(row[self._first_col]) <= 0:
+            raise AssertionError("At least the first FASTQ file is required.")
+        self._validate_fastq_format(row[self._first_col])
+
+    def _validate_second(self, row):
+        """Assert that the second FASTQ entry has the right format if it exists."""
+        if len(row[self._second_col]) > 0:
+            self._validate_fastq_format(row[self._second_col])
+
+    def _validate_pair(self, row):
+        """Assert that read pairs have the same file extension. Report pair status."""
+        if row[self._first_col] and row[self._second_col]:
+            row[self._single_col] = False
+            first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
+            second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
+            if first_col_suffix != second_col_suffix:
+                raise AssertionError("FASTQ pairs must have the same file extensions.")
+        else:
+            row[self._single_col] = True
+
+    def _validate_fastq_format(self, filename):
+        """Assert that a given filename has one of the expected FASTQ extensions."""
+        if not any(filename.endswith(extension) for extension in self.VALID_FORMATS):
+            raise AssertionError(
+                f"The FASTQ file has an unrecognized extension: {filename}\n"
+                f"It should be one of: {', '.join(self.VALID_FORMATS)}"
+            )
+
+    def validate_unique_samples(self):
+        """
+        Assert that the combination of sample name and FASTQ filename is unique.
+
+        In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the
+        number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment.
+
+        """
+        if len(self._seen) != len(self.modified):
+            raise AssertionError("The pair of sample name and FASTQ must be unique.")
+        seen = Counter()
+        for row in self.modified:
+            sample = row[self._sample_col]
+            seen[sample] += 1
+            row[self._sample_col] = f"{sample}_T{seen[sample]}"
+
+
+def read_head(handle, num_lines=10):
+    """Read the specified number of lines from the current position in the file."""
+    lines = []
+    for idx, line in enumerate(handle):
+        if idx == num_lines:
+            break
+        lines.append(line)
+    return "".join(lines)
+
+
+def sniff_format(handle):
+    """
+    Detect the tabular format.
+
+    Args:
+        handle (text file): A handle to a `text file`_ object. The read position is
+        expected to be at the beginning (index 0).
+
+    Returns:
+        csv.Dialect: The detected tabular format.
+
+    .. _text file:
+        https://docs.python.org/3/glossary.html#term-text-file
+
+    """
+    peek = read_head(handle)
+    handle.seek(0)
+    sniffer = csv.Sniffer()
+    dialect = sniffer.sniff(peek)
+    return dialect
+
+
+def check_samplesheet(file_in, file_out):
+    """
+    Check that the tabular samplesheet has the structure expected by nf-core pipelines.
+
+    Validate the general shape of the table, expected columns, and each row. Also add
+    an additional column which records whether one or two FASTQ reads were found.
+
+    Args:
+        file_in (pathlib.Path): The given tabular samplesheet. The format can be either
+            CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``.
+        file_out (pathlib.Path): Where the validated and transformed samplesheet should
+            be created; always in CSV format.
+
+    Example:
+        This function checks that the samplesheet follows the following structure,
+        see also the `viral recon samplesheet`_::
+
+            sample,fastq_1,fastq_2
+            SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
+            SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
+            SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
+
+    .. _viral recon samplesheet:
+        https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+
+    """
+    required_columns = {"sample", "fastq_1", "fastq_2"}
+    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
+    with file_in.open(newline="") as in_handle:
+        reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
+        # Validate the existence of the expected header columns.
+        if not required_columns.issubset(reader.fieldnames):
+            req_cols = ", ".join(required_columns)
+            logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
+            sys.exit(1)
+        # Validate each row.
+        checker = RowChecker()
+        for i, row in enumerate(reader):
+            try:
+                checker.validate_and_transform(row)
+            except AssertionError as error:
+                logger.critical(f"{str(error)} On line {i + 2}.")
+                sys.exit(1)
+        checker.validate_unique_samples()
+    header = list(reader.fieldnames)
+    header.insert(1, "single_end")
+    # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
+    with file_out.open(mode="w", newline="") as out_handle:
+        writer = csv.DictWriter(out_handle, header, delimiter=",")
+        writer.writeheader()
+        for row in checker.modified:
+            writer.writerow(row)
+
+
+def parse_args(argv=None):
+    """Define and immediately parse command line arguments."""
+    parser = argparse.ArgumentParser(
+        description="Validate and transform a tabular samplesheet.",
+        epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv",
+    )
+    parser.add_argument(
+        "file_in",
+        metavar="FILE_IN",
+        type=Path,
+        help="Tabular input samplesheet in CSV or TSV format.",
+    )
+    parser.add_argument(
+        "file_out",
+        metavar="FILE_OUT",
+        type=Path,
+        help="Transformed output samplesheet in CSV format.",
+    )
+    parser.add_argument(
+        "-l",
+        "--log-level",
+        help="The desired log level (default WARNING).",
+        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
+        default="WARNING",
+    )
+    return parser.parse_args(argv)
+
+
+def main(argv=None):
+    """Coordinate argument parsing and program execution."""
+    args = parse_args(argv)
+    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
+    if not args.file_in.is_file():
+        logger.error(f"The given input file {args.file_in} was not found!")
+        sys.exit(2)
+    args.file_out.parent.mkdir(parents=True, exist_ok=True)
+    check_samplesheet(args.file_in, args.file_out)
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/conf/base.config b/conf/base.config
new file mode 100644
index 0000000..e8cacf7
--- /dev/null
+++ b/conf/base.config
@@ -0,0 +1,65 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    nf-core/createpanelrefs Nextflow base config file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    A 'blank slate' config file, appropriate for general use on most high performance
+    compute environments. Assumes that all software is installed and available on
+    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    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.
+    // TODO nf-core: Customise requirements for specific processes.
+    // 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'  ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high_memory {
+        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
+    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
+        cache = false
+    }
+}
diff --git a/conf/igenomes.config b/conf/igenomes.config
new file mode 100644
index 0000000..3f11437
--- /dev/null
+++ b/conf/igenomes.config
@@ -0,0 +1,440 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines reference genomes using iGenome paths.
+    Can be used by any config that customises the base path using:
+        $params.igenomes_base / --igenomes_base
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    // illumina iGenomes reference file paths
+    genomes {
+        'GRCh37' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
+        }
+        'GRCh38' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+        }
+        'CHM13' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
+            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            mito_name   = "chrM"
+        }
+        'GRCm38' {
+            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "1.87e9"
+            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
+        }
+        'TAIR10' {
+            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+            mito_name   = "Mt"
+        }
+        'EB2' {
+            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
+        }
+        'UMD3.1' {
+            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'WBcel235' {
+            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
+            mito_name   = "MtDNA"
+            macs_gsize  = "9e7"
+        }
+        'CanFam3.1' {
+            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'GRCz10' {
+            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'BDGP6' {
+            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
+            mito_name   = "M"
+            macs_gsize  = "1.2e8"
+        }
+        'EquCab2' {
+            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'EB1' {
+            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
+        }
+        'Galgal4' {
+            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'Gm01' {
+            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+        }
+        'Mmul_1' {
+            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'IRGSP-1.0' {
+            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
+            mito_name   = "Mt"
+        }
+        'CHIMP2.1.4' {
+            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'Rnor_5.0' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'Rnor_6.0' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+        }
+        'R64-1-1' {
+            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            macs_gsize  = "1.2e7"
+        }
+        'EF2' {
+            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "1.21e7"
+        }
+        'Sbi1' {
+            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+        }
+        'Sscrofa10.2' {
+            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+            mito_name   = "MT"
+        }
+        'AGPv3' {
+            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
+            mito_name   = "Mt"
+        }
+        'hg38' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+        }
+        'hg19' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
+        }
+        'mm10' {
+            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "1.87e9"
+            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
+        }
+        'bosTau8' {
+            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+        }
+        'ce10' {
+            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "9e7"
+        }
+        'canFam3' {
+            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
+            mito_name   = "chrM"
+        }
+        'danRer10' {
+            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "1.37e9"
+        }
+        'dm6' {
+            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "1.2e8"
+        }
+        'equCab2' {
+            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
+            mito_name   = "chrM"
+        }
+        'galGal4' {
+            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
+            mito_name   = "chrM"
+        }
+        'panTro4' {
+            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
+            mito_name   = "chrM"
+        }
+        'rn6' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+        }
+        'sacCer3' {
+            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
+            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "1.2e7"
+        }
+        'susScr3' {
+            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
+            mito_name   = "chrM"
+        }
+    }
+}
diff --git a/conf/modules.config b/conf/modules.config
new file mode 100644
index 0000000..da58a5d
--- /dev/null
+++ b/conf/modules.config
@@ -0,0 +1,41 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: SAMPLESHEET_CHECK {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: FASTQC {
+        ext.args = '--quiet'
+    }
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
+}
diff --git a/conf/test.config b/conf/test.config
new file mode 100644
index 0000000..e307fb2
--- /dev/null
+++ b/conf/test.config
@@ -0,0 +1,29 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/createpanelrefs -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+
+    // Genome references
+    genome = 'R64-1-1'
+}
diff --git a/conf/test_full.config b/conf/test_full.config
new file mode 100644
index 0000000..3a7e17d
--- /dev/null
+++ b/conf/test_full.config
@@ -0,0 +1,24 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running full-size tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/createpanelrefs -profile test_full,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Full test profile'
+    config_profile_description = 'Full test dataset to check pipeline function'
+
+    // Input data for full size test
+    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+
+    // Genome references
+    genome = 'R64-1-1'
+}
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 0000000..e6d7bec
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,10 @@
+# nf-core/createpanelrefs: Documentation
+
+The nf-core/createpanelrefs documentation is split into the following pages:
+
+- [Usage](usage.md)
+  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
+- [Output](output.md)
+  - An overview of the different results produced by the pipeline and how to interpret them.
+
+You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
new file mode 100755
index 0000000..361d0e4
Binary files /dev/null and b/docs/images/mqc_fastqc_adapter.png differ
diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png
new file mode 100755
index 0000000..cb39ebb
Binary files /dev/null and b/docs/images/mqc_fastqc_counts.png differ
diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png
new file mode 100755
index 0000000..a4b89bf
Binary files /dev/null and b/docs/images/mqc_fastqc_quality.png differ
diff --git a/docs/images/nf-core-createpanelrefs_logo_dark.png b/docs/images/nf-core-createpanelrefs_logo_dark.png
new file mode 100644
index 0000000..017c368
Binary files /dev/null and b/docs/images/nf-core-createpanelrefs_logo_dark.png differ
diff --git a/docs/images/nf-core-createpanelrefs_logo_light.png b/docs/images/nf-core-createpanelrefs_logo_light.png
new file mode 100644
index 0000000..e73f972
Binary files /dev/null and b/docs/images/nf-core-createpanelrefs_logo_light.png differ
diff --git a/docs/output.md b/docs/output.md
new file mode 100644
index 0000000..b9d6a63
--- /dev/null
+++ b/docs/output.md
@@ -0,0 +1,68 @@
+# nf-core/createpanelrefs: Output
+
+## Introduction
+
+This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
+
+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.
+
+<!-- TODO nf-core: Write this documentation describing your workflow's output -->
+
+## Pipeline overview
+
+The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
+
+- [FastQC](#fastqc) - Raw read QC
+- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+
+### FastQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fastqc/`
+  - `*_fastqc.html`: FastQC report containing quality metrics.
+  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+
+</details>
+
+[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)
+
+![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
+
+![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
+
+> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+
+### MultiQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `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.
+
+</details>
+
+[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising 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.
+
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `pipeline_info/`
+  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+
+</details>
+
+[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/docs/usage.md b/docs/usage.md
new file mode 100644
index 0000000..359496c
--- /dev/null
+++ b/docs/usage.md
@@ -0,0 +1,216 @@
+# nf-core/createpanelrefs: Usage
+
+## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/createpanelrefs/usage](https://nf-co.re/createpanelrefs/usage)
+
+> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
+
+## Introduction
+
+<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
+
+## Samplesheet input
+
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+
+```bash
+--input '[path to samplesheet file]'
+```
+
+### Multiple runs of the same sample
+
+The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
+
+```console
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
+CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
+```
+
+### Full samplesheet
+
+The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below.
+
+A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice.
+
+```console
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
+CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
+TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,
+TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,
+TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,
+TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,
+```
+
+| Column    | Description                                                                                                                                                                            |
+| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `sample`  | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
+| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             |
+
+An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
+
+## Running the pipeline
+
+The typical command for running the pipeline is as follows:
+
+```bash
+nextflow run nf-core/createpanelrefs --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+```
+
+This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
+
+Note that the pipeline will create the following files in your working directory:
+
+```bash
+work                # Directory containing the nextflow working files
+<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.
+```
+
+If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
+
+Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
+
+> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+
+The above pipeline run specified with a params file in yaml format:
+
+```bash
+nextflow run nf-core/createpanelrefs -profile docker -params-file params.yaml
+```
+
+with `params.yaml` containing:
+
+```yaml
+input: './samplesheet.csv'
+outdir: './results/'
+genome: 'GRCh37'
+<...>
+```
+
+You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
+
+### Updating the pipeline
+
+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:
+
+```bash
+nextflow pull nf-core/createpanelrefs
+```
+
+### Reproducibility
+
+It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+
+First, go to the [nf-core/createpanelrefs releases page](https://github.com/nf-core/createpanelrefs/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
+
+To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+
+> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+
+## Core Nextflow arguments
+
+> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+
+### `-profile`
+
+Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
+
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
+
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+
+Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
+They are loaded in sequence, so later profiles can overwrite earlier profiles.
+
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+
+- `test`
+  - A profile with a complete configuration for automated testing
+  - Includes links to test data so needs no other parameters
+- `docker`
+  - A generic configuration profile to be used with [Docker](https://docker.com/)
+- `singularity`
+  - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
+- `podman`
+  - A generic configuration profile to be used with [Podman](https://podman.io/)
+- `shifter`
+  - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
+- `charliecloud`
+  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+- `apptainer`
+  - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `conda`
+  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
+
+### `-resume`
+
+Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html).
+
+You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
+
+### `-c`
+
+Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
+
+## Custom configuration
+
+### Resource requests
+
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+
+To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
+
+### Custom Containers
+
+In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+
+To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
+
+### Custom Tool Arguments
+
+A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
+
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
+
+### nf-core/configs
+
+In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
+
+See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
+
+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.
+
+The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.
+
+Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
+Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
+
+## Nextflow memory requirements
+
+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`):
+
+```bash
+NXF_OPTS='-Xms1g -Xmx4g'
+```
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
new file mode 100755
index 0000000..408951a
--- /dev/null
+++ b/lib/NfcoreTemplate.groovy
@@ -0,0 +1,336 @@
+//
+// This file holds several functions used within the nf-core pipeline template.
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class NfcoreTemplate {
+
+    //
+    // Check AWS Batch related parameters have been specified correctly
+    //
+    public static void awsBatch(workflow, params) {
+        if (workflow.profile.contains('awsbatch')) {
+            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
+            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+            // Check outdir paths to be S3 buckets if running on AWSBatch
+            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+        }
+    }
+
+    //
+    //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+    //
+    public static void checkConfigProvided(workflow, log) {
+        if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+            log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
+                    "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
+                    "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
+                    "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
+                    "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
+                    "Please refer to the quick start section and usage docs for the pipeline.\n "
+        }
+    }
+
+    //
+    // Generate version string
+    //
+    public static String version(workflow) {
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
+
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
+
+        return version_string
+    }
+
+    //
+    // Construct and send completion email
+    //
+    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
+
+        // Set up the e-mail variables
+        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+        if (!workflow.success) {
+            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        }
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['Date Started']              = workflow.start
+        misc_fields['Date Completed']            = workflow.complete
+        misc_fields['Pipeline script file path'] = workflow.scriptFile
+        misc_fields['Pipeline script hash ID']   = workflow.scriptId
+        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+        misc_fields['Nextflow Version']           = workflow.nextflow.version
+        misc_fields['Nextflow Build']             = workflow.nextflow.build
+        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+        def email_fields = [:]
+        email_fields['version']      = NfcoreTemplate.version(workflow)
+        email_fields['runName']      = workflow.runName
+        email_fields['success']      = workflow.success
+        email_fields['dateComplete'] = workflow.complete
+        email_fields['duration']     = workflow.duration
+        email_fields['exitStatus']   = workflow.exitStatus
+        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        email_fields['commandLine']  = workflow.commandLine
+        email_fields['projectDir']   = workflow.projectDir
+        email_fields['summary']      = summary << misc_fields
+
+        // On success try attach the multiqc report
+        def mqc_report = null
+        try {
+            if (workflow.success) {
+                mqc_report = multiqc_report.getVal()
+                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                    if (mqc_report.size() > 1) {
+                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    }
+                    mqc_report = mqc_report[0]
+                }
+            }
+        } catch (all) {
+            if (multiqc_report) {
+                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            }
+        }
+
+        // Check if we are only sending emails on failure
+        def email_address = params.email
+        if (!params.email && params.email_on_fail && !workflow.success) {
+            email_address = params.email_on_fail
+        }
+
+        // Render the TXT template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def tf           = new File("$projectDir/assets/email_template.txt")
+        def txt_template = engine.createTemplate(tf).make(email_fields)
+        def email_txt    = txt_template.toString()
+
+        // Render the HTML template
+        def hf            = new File("$projectDir/assets/email_template.html")
+        def html_template = engine.createTemplate(hf).make(email_fields)
+        def email_html    = html_template.toString()
+
+        // Render the sendmail template
+        def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
+        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+        def sendmail_html          = sendmail_template.toString()
+
+        // Send the HTML e-mail
+        Map colors = logColours(params.monochrome_logs)
+        if (email_address) {
+            try {
+                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+                // Try to send HTML e-mail using sendmail
+                [ 'sendmail', '-t' ].execute() << sendmail_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+            } catch (all) {
+                // Catch failures and try with plaintext
+                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                    mail_cmd += [ '-A', mqc_report ]
+                }
+                mail_cmd.execute() << email_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            }
+        }
+
+        // Write summary e-mail HTML to a file
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+        def output_hf = new File(output_d, "pipeline_report.html")
+        output_hf.withWriter { w -> w << email_html }
+        def output_tf = new File(output_d, "pipeline_report.txt")
+        output_tf.withWriter { w -> w << email_txt }
+    }
+
+    //
+    // Construct and send a notification to a web server as JSON
+    // e.g. Microsoft Teams and Slack
+    //
+    public static void IM_notification(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']      = NfcoreTemplate.version(workflow)
+        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.replaceFirst(/ +--hook_url +[^ ]+/, "")
+        msg_fields['projectDir']   = workflow.projectDir
+        msg_fields['summary']      = summary << misc_fields
+
+        // Render the JSON template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        // Different JSON depending on the service provider
+        // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+        def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+        def hf            = new File("$projectDir/assets/${json_path}")
+        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
+    //
+    public static void summary(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        if (workflow.success) {
+            if (workflow.stats.ignoredCount == 0) {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+            } else {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            }
+        } else {
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+        }
+    }
+
+    //
+    // ANSII Colours used for terminal logging
+    //
+    public static Map logColours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+
+        // Reset / Meta
+        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+        // Regular Colors
+        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+        // Bold
+        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+        // Underline
+        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+        // High Intensity
+        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+        // Bold High Intensity
+        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+        return colorcodes
+    }
+
+    //
+    // Does what is says on the tin
+    //
+    public static String dashedLine(monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    //
+    // nf-core logo
+    //
+    public static String logo(workflow, monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        String workflow_version = NfcoreTemplate.version(workflow)
+        String.format(
+            """\n
+            ${dashedLine(monochrome_logs)}
+                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
+            ${dashedLine(monochrome_logs)}
+            """.stripIndent()
+        )
+    }
+}
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
new file mode 100644
index 0000000..8d030f4
--- /dev/null
+++ b/lib/Utils.groovy
@@ -0,0 +1,47 @@
+//
+// This file holds several Groovy functions that could be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class Utils {
+
+    //
+    // When running with -profile conda, warn if channels have not been set-up appropriately
+    //
+    public static void checkCondaChannels(log) {
+        Yaml parser = new Yaml()
+        def channels = []
+        try {
+            def config = parser.load("conda config --show channels".execute().text)
+            channels = config.channels
+        } catch(NullPointerException | IOException e) {
+            log.warn "Could not verify conda channel configuration."
+            return
+        }
+
+        // Check that all channels are present
+        // 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
+        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 (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/\n" +
+                "  The observed channel order is \n" +
+                "  ${channels}\n" +
+                "  but the following channel order is required:\n" +
+                "  ${required_channels_in_order}\n" +
+                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        }
+    }
+}
diff --git a/lib/WorkflowCreatepanelrefs.groovy b/lib/WorkflowCreatepanelrefs.groovy
new file mode 100755
index 0000000..037c416
--- /dev/null
+++ b/lib/WorkflowCreatepanelrefs.groovy
@@ -0,0 +1,122 @@
+//
+// This file holds several functions specific to the workflow/createpanelrefs.nf in the nf-core/createpanelrefs pipeline
+//
+
+import nextflow.Nextflow
+import groovy.text.SimpleTemplateEngine
+
+class WorkflowCreatepanelrefs {
+
+    //
+    // Check and validate parameters
+    //
+    public static void initialise(params, log) {
+
+        genomeExistsError(params, log)
+
+
+        if (!params.fasta) {
+            Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+        }
+    }
+
+    //
+    // Get workflow summary for MultiQC
+    //
+    public static String paramsSummaryMultiqc(workflow, summary) {
+        String summary_section = ''
+        for (group in summary.keySet()) {
+            def group_params = summary.get(group)  // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                for (param in group_params.keySet()) {
+                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+        yaml_file_text        += "plot_type: 'html'\n"
+        yaml_file_text        += "data: |\n"
+        yaml_file_text        += "${summary_section}"
+        return yaml_file_text
+    }
+
+    //
+    // Generate methods description for MultiQC
+    //
+
+    public static String toolCitationText(params) {
+
+        // TODO Optionally add in-text citation tools to this list.
+        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+        // Uncomment function in methodsDescriptionText to render in MultiQC report
+        def citation_text = [
+                "Tools used in the workflow included:",
+                "FastQC (Andrews 2010),",
+                "MultiQC (Ewels et al. 2016)",
+                "."
+            ].join(' ').trim()
+
+        return citation_text
+    }
+
+    public static String toolBibliographyText(params) {
+
+        // TODO Optionally add bibliographic entries to this list.
+        // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
+        // Uncomment function in methodsDescriptionText to render in MultiQC report
+        def reference_text = [
+                "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+                "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+            ].join(' ').trim()
+
+        return reference_text
+    }
+
+    public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
+        // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+        def meta = [:]
+        meta.workflow = run_workflow.toMap()
+        meta["manifest_map"] = run_workflow.manifest.toMap()
+
+        // Pipeline DOI
+        meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
+        meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+
+        // Tool references
+        meta["tool_citations"] = ""
+        meta["tool_bibliography"] = ""
+
+        // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+        //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+        //meta["tool_bibliography"] = toolBibliographyText(params)
+
+
+        def methods_text = mqc_methods_yaml.text
+
+        def engine =  new SimpleTemplateEngine()
+        def description_html = engine.createTemplate(methods_text).make(meta)
+
+        return description_html
+    }
+
+    //
+    // Exit pipeline if incorrect --genome key provided
+    //
+    private static void genomeExistsError(params, log) {
+        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+            def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+                "  Currently, the available genome keys are:\n" +
+                "  ${params.genomes.keySet().join(", ")}\n" +
+                "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+            Nextflow.error(error_string)
+        }
+    }
+}
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
new file mode 100755
index 0000000..3a7b45c
--- /dev/null
+++ b/lib/WorkflowMain.groovy
@@ -0,0 +1,63 @@
+//
+// This file holds several functions specific to the main.nf workflow in the nf-core/createpanelrefs pipeline
+//
+
+import nextflow.Nextflow
+
+class WorkflowMain {
+
+    //
+    // Citation string for pipeline
+    //
+    public static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            // TODO nf-core: Add Zenodo DOI for pipeline after first release
+            //"* The pipeline\n" +
+            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
+
+    //
+    // Validate parameters and print summary to screen
+    //
+    public static void initialise(workflow, params, log) {
+
+        // Print workflow version and exit on --version
+        if (params.version) {
+            String workflow_version = NfcoreTemplate.version(workflow)
+            log.info "${workflow.manifest.name} ${workflow_version}"
+            System.exit(0)
+        }
+
+        // Check that a -profile or Nextflow config has been provided to run the pipeline
+        NfcoreTemplate.checkConfigProvided(workflow, log)
+
+        // Check that conda channels are set-up correctly
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+            Utils.checkCondaChannels(log)
+        }
+
+        // Check AWS batch settings
+        NfcoreTemplate.awsBatch(workflow, params)
+
+        // Check input has been provided
+        if (!params.input) {
+            Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
+        }
+    }
+    //
+    // Get attribute from genome config file e.g. fasta
+    //
+    public static Object getGenomeAttribute(params, attribute) {
+        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+            if (params.genomes[ params.genome ].containsKey(attribute)) {
+                return params.genomes[ params.genome ][ attribute ]
+            }
+        }
+        return null
+    }
+}
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
new file mode 100644
index 0000000..805c8bb
Binary files /dev/null and b/lib/nfcore_external_java_deps.jar differ
diff --git a/main.nf b/main.nf
new file mode 100644
index 0000000..b6f4193
--- /dev/null
+++ b/main.nf
@@ -0,0 +1,79 @@
+#!/usr/bin/env nextflow
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    nf-core/createpanelrefs
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Github : https://github.com/nf-core/createpanelrefs
+    Website: https://nf-co.re/createpanelrefs
+    Slack  : https://nfcore.slack.com/channels/createpanelrefs
+----------------------------------------------------------------------------------------
+*/
+
+nextflow.enable.dsl = 2
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    GENOME PARAMETER VALUES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    VALIDATE & PRINT PARAMETER SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+
+// Print help message if needed
+if (params.help) {
+    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
+    System.exit(0)
+}
+
+// Validate input parameters
+if (params.validate_params) {
+    validateParameters()
+}
+
+WorkflowMain.initialise(workflow, params, log)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOW FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { CREATEPANELREFS } from './workflows/createpanelrefs'
+
+//
+// WORKFLOW: Run main nf-core/createpanelrefs analysis pipeline
+//
+workflow NFCORE_CREATEPANELREFS {
+    CREATEPANELREFS ()
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN ALL WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// WORKFLOW: Execute a single named workflow for the pipeline
+// See: https://github.com/nf-core/rnaseq/issues/619
+//
+workflow {
+    NFCORE_CREATEPANELREFS ()
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
diff --git a/modules.json b/modules.json
new file mode 100644
index 0000000..fa09921
--- /dev/null
+++ b/modules.json
@@ -0,0 +1,27 @@
+{
+    "name": "nf-core/createpanelrefs",
+    "homePage": "https://github.com/nf-core/createpanelrefs",
+    "repos": {
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "installed_by": ["modules"]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "installed_by": ["modules"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
new file mode 100644
index 0000000..7ae3540
--- /dev/null
+++ b/modules/local/samplesheet_check.nf
@@ -0,0 +1,31 @@
+process SAMPLESHEET_CHECK {
+    tag "$samplesheet"
+    label 'process_single'
+
+    conda "conda-forge::python=3.8.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
+        'biocontainers/python:3.8.3' }"
+
+    input:
+    path samplesheet
+
+    output:
+    path '*.csv'       , emit: csv
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script: // This script is bundled with the pipeline, in nf-core/createpanelrefs/bin/
+    """
+    check_samplesheet.py \\
+        $samplesheet \\
+        samplesheet.valid.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
new file mode 100644
index 0000000..800a609
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -0,0 +1,24 @@
+process CUSTOM_DUMPSOFTWAREVERSIONS {
+    label 'process_single'
+
+    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
+    conda "bioconda::multiqc=1.14"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.yml"    , emit: yml
+    path "software_versions_mqc.yml", emit: mqc_yml
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    template 'dumpsoftwareversions.py'
+}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
new file mode 100644
index 0000000..c32657d
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -0,0 +1,36 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: custom_dumpsoftwareversions
+description: Custom module used to dump software versions within the nf-core pipeline template
+keywords:
+  - custom
+  - dump
+  - 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"
+  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
new file mode 100755
index 0000000..e55b8d4
--- /dev/null
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
+import platform
+from textwrap import dedent
+
+import yaml
+
+
+def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
+    html = [
+        dedent(
+            """\\
+            <style>
+            #nf-core-versions tbody:nth-child(even) {
+                background-color: #f2f2f2;
+            }
+            </style>
+            <table class="table" style="width:100%" id="nf-core-versions">
+                <thead>
+                    <tr>
+                        <th> Process Name </th>
+                        <th> Software </th>
+                        <th> Version  </th>
+                    </tr>
+                </thead>
+            """
+        )
+    ]
+    for process, tmp_versions in sorted(versions.items()):
+        html.append("<tbody>")
+        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+            html.append(
+                dedent(
+                    f"""\\
+                    <tr>
+                        <td><samp>{process if (i == 0) else ''}</samp></td>
+                        <td><samp>{tool}</samp></td>
+                        <td><samp>{version}</samp></td>
+                    </tr>
+                    """
+                )
+            )
+        html.append("</tbody>")
+    html.append("</table>")
+    return "\\n".join(html)
+
+
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
new file mode 100644
index 0000000..9ae5838
--- /dev/null
+++ b/modules/nf-core/fastqc/main.nf
@@ -0,0 +1,51 @@
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::fastqc=0.11.9"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
+        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
new file mode 100644
index 0000000..4da5bb5
--- /dev/null
+++ b/modules/nf-core/fastqc/meta.yml
@@ -0,0 +1,52 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+  - quality control
+  - qc
+  - adapters
+  - fastq
+tools:
+  - fastqc:
+      description: |
+        FastQC gives general quality metrics about your reads.
+        It provides information about the quality score distribution
+        across your reads, the per base sequence content (%A/C/G/T).
+        You get information about adapter contamination and other
+        overrepresented sequences.
+      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+      licence: ["GPL-2.0-only"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: FastQC report
+      pattern: "*_{fastqc.html}"
+  - zip:
+      type: file
+      description: FastQC report archive
+      pattern: "*_{fastqc.zip}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@grst"
+  - "@ewels"
+  - "@FelixKrueger"
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
new file mode 100644
index 0000000..4b60474
--- /dev/null
+++ b/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,53 @@
+process MULTIQC {
+    label 'process_single'
+
+    conda "bioconda::multiqc=1.14"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+
+    input:
+    path  multiqc_files, stageAs: "?/*"
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+
+    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
+
+    script:
+    def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    """
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $extra_config \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
new file mode 100644
index 0000000..f93b5ee
--- /dev/null
+++ b/modules/nf-core/multiqc/meta.yml
@@ -0,0 +1,56 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+
+input:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+
+output:
+  - report:
+      type: file
+      description: MultiQC report file
+      pattern: "multiqc_report.html"
+  - data:
+      type: directory
+      description: MultiQC data dir
+      pattern: "multiqc_data"
+  - plots:
+      type: file
+      description: Plots created by MultiQC
+      pattern: "*_data"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/nextflow.config b/nextflow.config
new file mode 100644
index 0000000..1c2fc1c
--- /dev/null
+++ b/nextflow.config
@@ -0,0 +1,269 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    nf-core/createpanelrefs Nextflow config file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Default config options for all compute environments
+----------------------------------------------------------------------------------------
+*/
+
+// Global default params, used in configs
+params {
+
+    // TODO nf-core: Specify your pipeline's command line flags
+    // Input options
+    input                      = null
+    // References
+    genome                     = null
+    igenomes_base              = 's3://ngi-igenomes/igenomes'
+    igenomes_ignore            = false
+    
+
+    // MultiQC options
+    multiqc_config             = null
+    multiqc_title              = null
+    multiqc_logo               = null
+    max_multiqc_email_size     = '25.MB'
+    multiqc_methods_description = null
+
+    // Boilerplate options
+    outdir                     = null
+    publish_dir_mode           = 'copy'
+    email                      = null
+    email_on_fail              = null
+    plaintext_email            = false
+    monochrome_logs            = false
+    hook_url                   = null
+    help                       = false
+    version                    = false
+
+    // Config options
+    config_profile_name        = null
+    config_profile_description = null
+    custom_config_version      = 'master'
+    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact     = null
+    config_profile_url         = null
+    
+
+    // Max resource options
+    // Defaults only, expecting to be overwritten
+    max_memory                 = '128.GB'
+    max_cpus                   = 16
+    max_time                   = '240.h'
+
+    // Schema validation default options
+    validationFailUnrecognisedParams = false
+    validationLenientMode            = false
+    validationSchemaIgnoreParams     = 'genomes'
+    validationShowHiddenParams       = false
+    validate_params                  = true
+
+}
+
+// Load base.config by default for all pipelines
+includeConfig 'conf/base.config'
+
+// Load nf-core custom profiles from different Institutions
+try {
+    includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
+
+// Load nf-core/createpanelrefs custom profiles from different institutions.
+// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// try {
+//   includeConfig "${params.custom_config_base}/pipeline/createpanelrefs.config"
+// } catch (Exception e) {
+//   System.err.println("WARNING: Could not load nf-core/config/createpanelrefs profiles: ${params.custom_config_base}/pipeline/createpanelrefs.config")
+// }
+profiles {
+    debug {
+        dumpHashes             = true
+        process.beforeScript   = 'echo $HOSTNAME'
+        cleanup                = false
+    }
+    conda {
+        conda.enabled          = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    mamba {
+        conda.enabled          = true
+        conda.useMamba         = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    docker {
+        docker.enabled         = true
+        docker.userEmulation   = true
+        conda.enabled          = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    arm {
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+    }
+    singularity {
+        singularity.enabled    = true
+        singularity.autoMounts = true
+        conda.enabled          = false
+        docker.enabled         = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    podman {
+        podman.enabled         = true
+        conda.enabled          = false
+        docker.enabled         = false
+        singularity.enabled    = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    shifter {
+        shifter.enabled        = true
+        conda.enabled          = false
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
+    }
+    charliecloud {
+        charliecloud.enabled   = true
+        conda.enabled          = false
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        apptainer.enabled      = false
+    }
+    apptainer {
+        apptainer.enabled      = true
+        conda.enabled          = false
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    gitpod {
+        executor.name          = 'local'
+        executor.cpus          = 16
+        executor.memory        = 60.GB
+    }
+    test      { includeConfig 'conf/test.config'      }
+    test_full { includeConfig 'conf/test_full.config' }
+}
+
+// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry   = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Nextflow plugins
+plugins {
+    id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+// Load igenomes.config if required
+if (!params.igenomes_ignore) {
+    includeConfig 'conf/igenomes.config'
+} else {
+    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.
+
+env {
+    PYTHONNOUSERSITE = 1
+    R_PROFILE_USER   = "/.Rprofile"
+    R_ENVIRON_USER   = "/.Renviron"
+    JULIA_DEPOT_PATH = "/usr/local/share/julia"
+}
+
+// Capture exit codes from upstream processes when piping
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+
+def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+timeline {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+}
+report {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+}
+trace {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+}
+dag {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+}
+
+manifest {
+    name            = 'nf-core/createpanelrefs'
+    author          = """@maxulysse"""
+    homePage        = 'https://github.com/nf-core/createpanelrefs'
+    description     = """Generate Panel of Normals, models or other similar references from lots of samples"""
+    mainScript      = 'main.nf'
+    nextflowVersion = '!>=23.04.0'
+    version         = '1.0dev'
+    doi             = ''
+}
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
+// Function to ensure that resource requirements don't go beyond
+// a maximum limit
+def check_max(obj, type) {
+    if (type == 'memory') {
+        try {
+            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+                return params.max_memory as nextflow.util.MemoryUnit
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'time') {
+        try {
+            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+                return params.max_time as nextflow.util.Duration
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'cpus') {
+        try {
+            return Math.min( obj, params.max_cpus as int )
+        } catch (all) {
+            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+            return obj
+        }
+    }
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
new file mode 100644
index 0000000..1972341
--- /dev/null
+++ b/nextflow_schema.json
@@ -0,0 +1,303 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/createpanelrefs/master/nextflow_schema.json",
+    "title": "nf-core/createpanelrefs pipeline parameters",
+    "description": "Generate Panel of Normals, models or other similar references from lots of samples",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["input", "outdir"],
+            "properties": {
+                "input": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/csv",
+                    "pattern": "^\\S+\\.csv$",
+                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/createpanelrefs/usage#samplesheet-input).",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "email": {
+                    "type": "string",
+                    "description": "Email address for completion summary.",
+                    "fa_icon": "fas fa-envelope",
+                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                },
+                "multiqc_title": {
+                    "type": "string",
+                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+                    "fa_icon": "fas fa-file-signature"
+                }
+            }
+        },
+        "reference_genome_options": {
+            "title": "Reference genome options",
+            "type": "object",
+            "fa_icon": "fas fa-dna",
+            "description": "Reference genome related files and options required for the workflow.",
+            "properties": {
+                "genome": {
+                    "type": "string",
+                    "description": "Name of iGenomes reference.",
+                    "fa_icon": "fas fa-book",
+                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+                },
+                "fasta": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+                    "description": "Path to FASTA genome file.",
+                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "Directory / URL base for iGenomes references.",
+                    "default": "s3://ngi-igenomes/igenomes",
+                    "fa_icon": "fas fa-cloud-download-alt",
+                    "hidden": true
+                },
+                "igenomes_ignore": {
+                    "type": "boolean",
+                    "description": "Do not load the iGenomes reference config.",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                }
+            }
+        },
+        "institutional_config_options": {
+            "title": "Institutional config options",
+            "type": "object",
+            "fa_icon": "fas fa-university",
+            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
+            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
+            "properties": {
+                "custom_config_version": {
+                    "type": "string",
+                    "description": "Git commit id for Institutional configs.",
+                    "default": "master",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
+                },
+                "custom_config_base": {
+                    "type": "string",
+                    "description": "Base directory for Institutional configs.",
+                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
+                    "hidden": true,
+                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
+                    "fa_icon": "fas fa-users-cog"
+                },
+                "config_profile_name": {
+                    "type": "string",
+                    "description": "Institutional config name.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
+                },
+                "config_profile_description": {
+                    "type": "string",
+                    "description": "Institutional config description.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
+                },
+                "config_profile_contact": {
+                    "type": "string",
+                    "description": "Institutional config contact information.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
+                },
+                "config_profile_url": {
+                    "type": "string",
+                    "description": "Institutional config URL link.",
+                    "hidden": true,
+                    "fa_icon": "fas fa-users-cog"
+                }
+            }
+        },
+        "max_job_request_options": {
+            "title": "Max job request options",
+            "type": "object",
+            "fa_icon": "fab fa-acquisitions-incorporated",
+            "description": "Set the top limit for requested resources for any single job.",
+            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
+            "properties": {
+                "max_cpus": {
+                    "type": "integer",
+                    "description": "Maximum number of CPUs that can be requested for any single job.",
+                    "default": 16,
+                    "fa_icon": "fas fa-microchip",
+                    "hidden": true,
+                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
+                },
+                "max_memory": {
+                    "type": "string",
+                    "description": "Maximum amount of memory that can be requested for any single job.",
+                    "default": "128.GB",
+                    "fa_icon": "fas fa-memory",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+                    "hidden": true,
+                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
+                },
+                "max_time": {
+                    "type": "string",
+                    "description": "Maximum amount of time that can be requested for any single job.",
+                    "default": "240.h",
+                    "fa_icon": "far fa-clock",
+                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
+                    "hidden": true,
+                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
+                }
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "help": {
+                    "type": "boolean",
+                    "description": "Display help text.",
+                    "fa_icon": "fas fa-question-circle",
+                    "default": false,
+                    "hidden": true
+                },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "default": false,
+                    "hidden": true
+                },
+                "publish_dir_mode": {
+                    "type": "string",
+                    "default": "copy",
+                    "description": "Method used to save pipeline results to output directory.",
+                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+                    "fa_icon": "fas fa-copy",
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "hidden": true
+                },
+                "email_on_fail": {
+                    "type": "string",
+                    "description": "Email address for completion summary, only when pipeline fails.",
+                    "fa_icon": "fas fa-exclamation-triangle",
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
+                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
+                    "hidden": true
+                },
+                "plaintext_email": {
+                    "type": "boolean",
+                    "description": "Send plain-text email instead of HTML.",
+                    "fa_icon": "fas fa-remove-format",
+                    "default": false,
+                    "hidden": true
+                },
+                "max_multiqc_email_size": {
+                    "type": "string",
+                    "description": "File size limit when attaching MultiQC reports to summary emails.",
+                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+                    "default": "25.MB",
+                    "fa_icon": "fas fa-file-upload",
+                    "hidden": true
+                },
+                "monochrome_logs": {
+                    "type": "boolean",
+                    "description": "Do not use coloured log outputs.",
+                    "fa_icon": "fas fa-palette",
+                    "default": false,
+                    "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, MS Teams and Slack are supported.",
+                    "hidden": true
+                },
+                "multiqc_config": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Custom config file to supply to MultiQC.",
+                    "fa_icon": "fas fa-cog",
+                    "hidden": true
+                },
+                "multiqc_logo": {
+                    "type": "string",
+                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
+                    "fa_icon": "fas fa-image",
+                    "hidden": true
+                },
+                "multiqc_methods_description": {
+                    "type": "string",
+                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
+                    "fa_icon": "fas fa-cog"
+                },
+                "validate_params": {
+                    "type": "boolean",
+                    "description": "Boolean whether to validate parameters against the schema at runtime",
+                    "default": true,
+                    "fa_icon": "fas fa-check-square",
+                    "hidden": true
+                },
+                "validationShowHiddenParams": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-eye-slash",
+                    "description": "Show all params when using `--help`",
+                    "default": false,
+                    "hidden": true,
+                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
+                },
+                "validationFailUnrecognisedParams": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
+                    "default": false,
+                    "hidden": true,
+                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
+                },
+                "validationLenientMode": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Validation of parameters in lenient more.",
+                    "default": false,
+                    "hidden": true,
+                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/reference_genome_options"
+        },
+        {
+            "$ref": "#/definitions/institutional_config_options"
+        },
+        {
+            "$ref": "#/definitions/max_job_request_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..0d62beb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
new file mode 100644
index 0000000..0aecf87
--- /dev/null
+++ b/subworkflows/local/input_check.nf
@@ -0,0 +1,44 @@
+//
+// Check input samplesheet and get read channels
+//
+
+include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
+
+workflow INPUT_CHECK {
+    take:
+    samplesheet // file: /path/to/samplesheet.csv
+
+    main:
+    SAMPLESHEET_CHECK ( samplesheet )
+        .csv
+        .splitCsv ( header:true, sep:',' )
+        .map { create_fastq_channel(it) }
+        .set { reads }
+
+    emit:
+    reads                                     // channel: [ val(meta), [ reads ] ]
+    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
+}
+
+// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
+def create_fastq_channel(LinkedHashMap row) {
+    // create meta map
+    def meta = [:]
+    meta.id         = row.sample
+    meta.single_end = row.single_end.toBoolean()
+
+    // add path(s) of the fastq file(s) to the meta map
+    def fastq_meta = []
+    if (!file(row.fastq_1).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
+    }
+    if (meta.single_end) {
+        fastq_meta = [ meta, [ file(row.fastq_1) ] ]
+    } else {
+        if (!file(row.fastq_2).exists()) {
+            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+        }
+        fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
+    }
+    return fastq_meta
+}
diff --git a/tower.yml b/tower.yml
new file mode 100644
index 0000000..787aedf
--- /dev/null
+++ b/tower.yml
@@ -0,0 +1,5 @@
+reports:
+  multiqc_report.html:
+    display: "MultiQC HTML report"
+  samplesheet.csv:
+    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
diff --git a/workflows/createpanelrefs.nf b/workflows/createpanelrefs.nf
new file mode 100644
index 0000000..4ab6d8b
--- /dev/null
+++ b/workflows/createpanelrefs.nf
@@ -0,0 +1,133 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PRINT PARAMS SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
+
+WorkflowCreatepanelrefs.initialise(params, log)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    CONFIG FILES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
+//
+include { INPUT_CHECK } from '../subworkflows/local/input_check'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// MODULE: Installed directly from nf-core/modules
+//
+include { FASTQC                      } from '../modules/nf-core/fastqc/main'
+include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// Info required for completion email and summary
+def multiqc_report = []
+
+workflow CREATEPANELREFS {
+
+    ch_versions = Channel.empty()
+
+    //
+    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    //
+    INPUT_CHECK (
+        file(params.input)
+    )
+    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+    // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
+    // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
+    // ! There is currently no tooling to help you write a sample sheet schema
+
+    //
+    // MODULE: Run FastQC
+    //
+    FASTQC (
+        INPUT_CHECK.out.reads
+    )
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+
+    CUSTOM_DUMPSOFTWAREVERSIONS (
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
+    )
+
+    //
+    // MODULE: MultiQC
+    //
+    workflow_summary    = WorkflowCreatepanelrefs.paramsSummaryMultiqc(workflow, summary_params)
+    ch_workflow_summary = Channel.value(workflow_summary)
+
+    methods_description    = WorkflowCreatepanelrefs.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
+    ch_methods_description = Channel.value(methods_description)
+
+    ch_multiqc_files = Channel.empty()
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+
+    MULTIQC (
+        ch_multiqc_files.collect(),
+        ch_multiqc_config.toList(),
+        ch_multiqc_custom_config.toList(),
+        ch_multiqc_logo.toList()
+    )
+    multiqc_report = MULTIQC.out.report.toList()
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    COMPLETION EMAIL AND SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow.onComplete {
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    }
+    NfcoreTemplate.summary(workflow, params, log)
+    if (params.hook_url) {
+        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
+    }
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/