Merge pull request #243 from nf-core/dev

v2.4.0 - Maroon Gold Boxer
nf-core · Dec 1, 2022 · a2235d5 · a2235d5
2 parents bc0a2dd + 19de3f4
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diff --git a/.editorconfig b/.editorconfig
@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mhcq
 
 - [ ] 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/mhcquant/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/mhcquant _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mhcquant/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/mhcquant _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -25,6 +25,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -23,6 +23,7 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/mhcquant'
         run: |
-          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/mhcquant ]] && [[ $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
@@ -42,4 +42,3 @@ jobs:
             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
@@ -10,7 +10,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
 
 jobs:
   test:
@@ -20,27 +19,17 @@ jobs:
     runs-on: ubuntu-latest
     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"
+        NXF_VER:
+          - "21.10.3"
+          - "latest-everything"
     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: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
         run: |

diff --git a/.github/workflows/fix-linting.yml 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/mhcquant'
+    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@v2
+
+      - 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 "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          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 "[email protected]"
+          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
@@ -35,22 +35,48 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies
@@ -78,5 +104,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-
-#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -26,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-#
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,5 +1 @@
 repository_type: pipeline
-
-lint:
-  files_exist:
-    - conf/igenomes.config
diff --git a/.prettierignore b/.prettierignore
@@ -0,0 +1,10 @@
+email_template.html
+adaptivecard.json
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,52 @@
 # nf-core/mhcquant: 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).
+
+## v2.4.0 nfcore/mhcquant "Maroon Gold Boxer" - 2022/12/02
+
+Initial release of nf-core/mhcquant, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+- Additional output from `CometAdapter` (generated with the parameter `--pin_out`)
+- Folder structure within the `intermediate_results` folder to retrace the outcome files easier
+- `OPENMS_FALSEDISCOVERYRATE` and `OPENMS_IDFILTER_FOR_ALIGNMENT` are now included in the first quantification step
+- Altered the outcome content with the inclusion of the different folder structure
+- Updated the mhcquant_web.png in the `assets` folder
+- [#229](https://github.com/nf-core/mhcquant/pull/229) Add ion annotation feature requested in [#220](https://github.com/nf-core/mhcquant/issues/220)
+- [#235](https://github.com/nf-core/mhcquant/issues/235) Add the `annotate_ions` parameter to enable/disable the ion annotation feature (default is false)
+
+### `Fixed`
+
+- Resolved issues with `SAMPLESHEET_CHECK`
+- Fix for the `peakpickerhires`, mzml files generated from input raw files are now seen as input for this step as well
+- `PRE_QUANTIFICATION` is renamed to `MAP_ALIGNMENT` to indicate that the alignment (and the complementing processes) of the different maps happens here
+- `POST_QUANTIFICATION` is renamed to `PROCESS_FEATURE` since the feature identification and processing is done here
+- Outcome of `OPENMS_FEATUREFINDERIDENTIFICATION` got lost during one of the previous updates, this is reintroduced
+- `OPENMS_TEXTEXPORTER_UNQUANTIFIED` and `OPENMS_TEXTEXPORTER_QUANTIFIED` return only significant hits again
+- [#226](https://github.com/nf-core/mhcquant/pull/226) - nf-core template update (version 2.6)
+- [#230](https://github.com/nf-core/mhcquant/issues/230) - Issue with `OPENMS_MZTABEXPORTER_QUANT`
+- [#236](https://github.com/nf-core/mhcquant/issues/236) - Resolved issue with `PYOPENMS_IONANNOTATOR`
+- Fix for an inconsistent mzml channel issue
+- [#241](https://github.com/nf-core/mhcquant/issues/241) - Fix of the HLA allele annotation in the help of the `allele_sheet` parameter
+
+### `Dependencies`
+
+- Updated the multiQC module
+
+| Dependency            | Old version | New version |
+| --------------------- | ----------- | ----------- |
+| `MultiQC`             | 1.11        | 1.12        |
+| `OpenMS`              | 2.6.0       | 2.8.0       |
+| `OpenMS thirdparty`   | 2.6.0       | 2.8.0       |
+| `pyOpenMS`            | -           | 2.8         |
+| `thermorawfileparser` | 1.3.4       | 1.4.0       |
+
+### `Deprecated`
+
+- `OPENMS_TEXTEXPORTER_PSMS` was removed due to the outcome of the comet adapter step
+
 ## v2.3.1 nfcore/mhcquant "White Gold Swallow" - 2022/05/10
 
 ### `Added`
@@ -20,7 +67,7 @@
 ### `Added`
 
 - [#206](https://github.com/nf-core/mhcquant/issues/206) Updated the workflow picture
-- Adjustments of the `PRE_QUANTIFICATION` subworkflow: `OPENMS_FALSEDISCOVERYRATE`, `OPENMS_IDFILTER_FOR_ALIGNMENT`, and `OPENMS_TEXTEXPORTER_PSMS`
+- Adjustments of the `PRE_QUANTIFICATION` subworkflow: `OPENMS_FALSEDISCOVERYRATE`, `OPENMS_IDFILTER_FOR_ALIGNMENT`, and `OPENMS_TEXTEXPORTER_SINGLE`
 - Included `OPENMS_TEXTEXPORTER_UNQUANTIFIED`to write a combined FDR filtered output file for unquantified data
 - Included `pipeline summary` and increment the `documentation` paragraph
 - [#195](https://github.com/nf-core/mhcquant/issues/195) Updated parameter documentation

diff --git a/README.md b/README.md
@@ -1,18 +1,14 @@
 # ![nf-core/mhcquant](docs/images/nf-core-mhcquant_logo_light.png#gh-light-mode-only) ![nf-core/mhcquant](docs/images/nf-core-mhcquant_logo_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/mhcquant/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/mhcquant/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mhcquant/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1569909-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1569909)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1569909-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1569909)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?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/mhcquant)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mhcquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mhcquant)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mhcquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mhcquant)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -36,7 +32,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run nf-core/mhcquant -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
@@ -86,7 +82,7 @@ Additional functionality contained by the pipeline currently includes:
 - Conversion of raw to mzML files (`ThermoRawFileParser`)
 - Executing the peak picking with high_res algorithm (`PeakPickerHiRes`)
 
-#### Prequantification
+#### Map alignment
 
 - Corrects retention time distortions between maps, using information from peptides identified in different maps (`MapAlignerIdentification`)
 - Applies retention time transformations to maps (`MapRTTransformer`)
@@ -97,12 +93,13 @@ Additional functionality contained by the pipeline currently includes:
 - Predict psm results using mhcflurry to shrink search space (`mhcflurry`)
 - Facilitates the input to, the call of and output integration of Percolator (`PercolatorAdapter`)
 
-#### Post-quantification
+#### Process features
 
 - Detects features in MS1 data based on peptide identifications (`FeatureFinderIdentification`)
 - Group corresponding features across labelfree experiments (`FeatureLinkerUnlabeledKD`)
 - Resolves ambiguous annotations of features with peptide identifications (`IDConflictResolver`)
 - Converts XML format to text files (`TextExporter`)
+- Annotates final list of peptides with their respective ions and charges (`IonAnnotator`)
 
 #### Prediction of HLA class 1 peptides
 
@@ -145,6 +142,7 @@ Helpful contributors:
 - [Christian Fufezan](https://github.com/fu)
 - [Sven Fillinger](https://github.com/sven1103)
 - [Kevin Menden](https://github.com/KevinMenden)
+- [Jonas Scheid](https://github.com/jonasscheid)
 
 ## Contributions and Support