Add strict syntax support

.github/workflows/awsfulltest.yml

@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/awstest.yml

@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/download_pipeline.yml

@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

.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@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

.github/workflows/nf-test.yml

@@ -27,7 +27,9 @@ env:
 jobs:
   nf-test-changes:
     name: nf-test-changes
-    runs-on: ubuntu-latest
+    runs-on: # use self-hosted runners
+      - runs-on=${{ github.run_id }}-nf-test-changes
+      - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
       total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -38,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -59,7 +61,9 @@ jobs:
     name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
-    runs-on: ubuntu-latest
+    runs-on: # use self-hosted runners
+      - runs-on=${{ github.run_id }}-nf-test
+      - runner=4cpu-linux-x64
     strategy:
       fail-fast: false
       matrix:
@@ -81,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -115,7 +119,9 @@ jobs:
   confirm-pass:
     needs: [nf-test]
     if: always()
-    runs-on: ubuntu-latest
+    runs-on: # use self-hosted runners
+      - runs-on=${{ github.run_id }}-confirm-pass
+      - runner=2cpu-linux-x64
     steps:
       - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}

.github/workflows/release-announcements.yml

@@ -15,10 +15,9 @@ jobs:
           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' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics

.github/workflows/template-version-comment.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

.nf-core.yml

@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/PULL_REQUEST_TEMPLATE.md
-nf_core_version: 3.4.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Fabiola Curion

.prettierignore

@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

README.md

@@ -5,13 +5,13 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/hadge)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/hadge)
 [![GitHub Actions CI Status](https://github.com/nf-core/hadge/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/hadge/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/hadge/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/hadge/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/hadge/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)
 [![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/)

modules.json

@@ -46,7 +46,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b",
                         "installed_by": ["modules"]
                     },
                     "multiseqdemux": {
@@ -123,7 +123,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

modules/local/extract_hashes/main.nf

@@ -17,7 +17,7 @@ process EXTRACT_HASHES {
     task.ext.when == null || task.ext.when
 
     script:
-    prefix         = task.ext.prefix         ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     gunzip -c ${hto_dir}/features.tsv.gz | awk '{print \$2}' | paste -sd, - > ${prefix}_hashes.txt
 

modules/local/hash_summary/main.nf

@@ -30,8 +30,8 @@ process HASH_SUMMARY {
     task.ext.when == null || task.ext.when
 
     script:
-    prefix         = task.ext.prefix         ?: "${meta.id}"
-    hash_list      = "${meta.hto_names}".split(",")
+    prefix = task.ext.prefix ?: "${meta.id}"
+    hash_list = "${meta.hto_names}".split(",")
 
     template 'hash_summary.py'
 

modules/local/htodemux_visualization/main.nf

@@ -51,7 +51,7 @@ process HTODEMUX_VISUALIZATION {
     heatMapNcells  = task.ext.heatMapNcells  ?: 500          // Number of cells for heatmap
 
     // Output Parameters
-    prefix         = task.ext.prefix         ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     template 'htodemux_visualization.R'
 

modules/local/preprocessing_for_htodemux_multiseq/main.nf

@@ -30,7 +30,7 @@ process PREPROCESSING_FOR_HTODEMUX_MULTISEQ {
     gene_col    = task.ext.gene_col    ?: 2               // Specify which column of genes.tsv or features.tsv to use for gene names
 
     // others
-    prefix      = task.ext.prefix      ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     template 'pre_processing.R'