Merge pull request #243 from christopher-mohr/merge-template-update-2…

…-14-1 Merge template updates up to 2.14.1
nf-core · May 16, 2024 · 0282263 · 0282263
2 parents 81fba13 + 16d714a
commit 0282263
Show file tree

Hide file tree

Showing 44 changed files with 225 additions and 432 deletions.
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/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/epit
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/epitopeprediction/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/epitopeprediction _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 (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ 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
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -30,7 +30,7 @@ jobs:
 
       - 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
@@ -5,13 +5,13 @@ 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
+      # 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 }}
@@ -27,7 +27,7 @@ jobs:
 
       - 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@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@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@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(.full_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/.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:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +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 - Bühl - 2024-03-28
+## v2.3.1 - Oesterberg - 2024-05-17
 
-### `Fixed`
+### `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
@@ -13,7 +13,7 @@
 [![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 Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](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/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
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -20,14 +20,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

diff --git a/conf/test.config b/conf/test.config
@@ -16,7 +16,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,6 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_full_test.csv'
+    input = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_full_test.csv'
     tools = 'syfpeithi,mhcflurry,mhcnuggets-class-1,mhcnuggets-class-2'
+
 }
diff --git a/conf/test_grch38.config b/conf/test_grch38.config
@@ -13,6 +13,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     genome_reference = 'grch38'
 }
diff --git a/conf/test_mhcflurry.config b/conf/test_mhcflurry.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     tools = 'mhcflurry'
 }
diff --git a/conf/test_mhcnuggets.config b/conf/test_mhcnuggets.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
     tools = 'mhcnuggets-class-1,mhcnuggets-class-2'
 }
diff --git a/conf/test_netmhc.config b/conf/test_netmhc.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhc-4.0'
     netmhc_path = './non-free/netmhc.tar.gz'

diff --git a/conf/test_netmhcii.config b/conf/test_netmhcii.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhcii-2.2'
     netmhcii_path = './non-free/netmhcii.tar.Z'

diff --git a/conf/test_netmhciipan.config b/conf/test_netmhciipan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhciipan-4.1'
     netmhciipan_path = './non-free/netmhciipan.tar.gz'

diff --git a/conf/test_netmhcpan.config b/conf/test_netmhcpan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhcpan-4.0'
     netmhcpan_path = './non-free/netmhcpan.tar.gz'

diff --git a/conf/test_peptides.config b/conf/test_peptides.config
@@ -13,5 +13,5 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 }