Merge pull request #183 from nf-core/dev

Prepare for version 2.2 "Silver Titanium Ostrich"

.gitattributes

@@ -1 +1,3 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -68,16 +68,13 @@ 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 flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
-6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
-7. Add sanity checks for all relevant parameters.
-8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+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.yaml` 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
 
@@ -102,27 +99,6 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 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]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### 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/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,52 @@
+
+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/mhcquant pipeline documentation](https://nf-co.re/mhcquant/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. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/mhcquant _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/mhcquant 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

.github/workflows/awsfulltest.yml

@@ -20,11 +20,11 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
-          revision: ${{ github.sha } }
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test_full,aws_tower
           pre_run_script: 'export NXF_VER=21.10.3'

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v2
-
+        
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -22,7 +22,7 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
           pre_run_script: 'export NXF_VER=21.10.3'

.github/workflows/ci.yml

@@ -8,29 +8,36 @@ on:
   release:
     types: [published]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
 
 jobs:
   test:
     name: Run workflow tests
     # 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/mhcquant') }}
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.10.3', '']
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
@@ -44,17 +51,30 @@ jobs:
     # 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/mhcquant') }}
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+
       - name: Run pipeline with additional params
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT

.github/workflows/linting_comment.yml

@@ -15,6 +15,7 @@ jobs:
         uses: dawidd6/action-download-artifact@v2
         with:
           workflow: linting.yml
+          workflow_conclusion: completed
 
       - name: Get PR number
         id: pr_number

CHANGELOG.md

@@ -1,5 +1,29 @@
 # nf-core/mhcquant: Changelog
 
+## v2.2.0 nfcore/mhcquant "Silver Titanium Ostrich" - 2021/01/14
+
+### `Added`
+
+- Included the newest nf-core template (version 2.2)
+- Adjustment of the README, including all contributors
+- Inclusion of the PSMs files (tsv format) per replicates in `results/PSMs`
+- Include check in WorkflowMhcquant, to determine if the allele and vcf sheet has been provided under specific circumstances
+
+### `Fixed`
+
+- Changed parameters in the nextflow_schema.json to be in coherence with the nextflow.config
+- Error that was raised in generate_proteins_from_vcf
+- Problems that were detected in predict_possible_class1_neoepitopes and predict_possible_class2_neoepitopes
+- Error that occurred in mhcnuggets_predictneoepitopesclass2 (faulty container set up)
+
+### `Dependencies`
+
+| Dependency            | Old version | New version |
+| --------------------- | ----------- | ----------- |
+| `fred2`              | 2.0.6       | 2.0.7       |
+
+### `Deprecated`
+
 ## v2.1.0 nf-core/mhcquant "Olive Tin Hamster" - 2021/12/09
 
 ### `Added`

CITATIONS.md

@@ -22,7 +22,7 @@
 * [OpenMS](https://pubmed.ncbi.nlm.nih.gov/27575624/)
     > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L,  Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13, 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624
 
-* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
+* [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