Merge pull request #238 from nf-core/dev

Release 2.3.1
nf-core · May 17, 2024 · cfbfeb5 · cfbfeb5
2 parents e173620 + 0282263
commit cfbfeb5
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -10,15 +10,7 @@
         "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"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

diff --git a/.editorconfig b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -9,9 +9,8 @@ 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 ;)
 
-:::info
-If you need help using or modifying nf-core/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 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.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 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.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -8,13 +8,13 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/epitopeprediction'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
+      - name: Launch workflow via Seqera Platform
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -28,9 +28,9 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -5,14 +5,14 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/epitopeprediction'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,9 +25,9 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

diff --git a/.gitpod.yml b/.gitpod.yml
@@ -10,13 +10,11 @@ tasks:
 
 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
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -4,3 +4,4 @@ lint:
     - assets/nf-core-epitopeprediction_logo_light.png
     - docs/images/nf-core-epitopeprediction_logo_light.png
     - docs/images/nf-core-epitopeprediction_logo_dark.png
+nf_core_version: "2.14.1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,17 @@
 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).
 
+## v2.3.1 - Oesterberg - 2024-05-17
+
+### `Changed`
+
+- [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Update to nf-core template `2.14.1`
+- [#237](https://github.com/nf-core/epitopeprediction/pull/237) - Update to nf-core template `2.13.1`
+
+### `Fixed`
+
+- [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Add check for protein map to prevent failure if no information is available
+
 ## v2.3.0 - Oesterberg - 2024-02-26
 
 ### `Changed`

diff --git a/README.md b/README.md
@@ -5,14 +5,15 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/epitopeprediction/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/epitopeprediction/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
+[![GitHub Actions CI Status](https://github.com/nf-core/epitopeprediction/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/epitopeprediction/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/epitopeprediction/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/epitopeprediction/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
+[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![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?labelColor=000000)](https://tower.nf/launch?pipeline=https://github.com/nf-core/epitopeprediction)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/epitopeprediction)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23epitopeprediction-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/epitopeprediction)[![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)
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/releases/tag/2.3.0" target="_blank">nf-core/epitopeprediction</a>
+  This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/releases/tag/2.3.1" target="_blank">nf-core/epitopeprediction</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/epitopeprediction/2.3.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/epitopeprediction/2.3.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-epitopeprediction-methods-description":

diff --git a/bin/epaa.py b/bin/epaa.py
@@ -425,6 +425,11 @@ def read_lig_ID_values(filename):
 
 def create_protein_column_value(pep):
     # retrieve Ensembl protein ID for given transcript IDs, if we want to provide additional protein ID types, adapt here
+    # we have to catch cases where no protein information is available, e.g. if there are issues on BioMart side
+    if transcriptProteinTable is None:
+        logger.warning(f"Protein mapping not available for peptide {str(pep)}")
+        return ""
+
     all_proteins = [
         # split by : otherwise epytope generator suffix included
         transcriptProteinTable.query(f'transcript_id == "{transcript.transcript_id.split(":")[0]}"')["ensembl_id"]

diff --git a/conf/base.config b/conf/base.config
@@ -53,7 +53,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }