test default nextflow and (without failing) latest-everything

.github/workflows/fix-linting.yml

@@ -13,13 +13,13 @@ 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@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -31,23 +31,27 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
+      # Setup nextflow for the linting step
+      - uses: nf-core/setup-nextflow@v2
+
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
-          python-version: 3.11
+          python-version: 3.14
 
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1
+        with:
+          install-only: true
 
       - name: Run pre-commit
         id: pre-commit
-        run: pre-commit run --all-files
+        run: prek run --all-files
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +71,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5.0.0
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |

.github/workflows/linting.yml

@@ -16,6 +16,6 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
-      - uses: pre-commit/action@v3.0.1
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: nf-core/setup-nextflow@v2
+      - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1

.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@5c98f0b039f36ef966fdb7dfa9779262785ecb05 # v14
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2.9.4
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Check if all profiles are tested
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: Check whether profiles are all tested
         run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
 
@@ -31,7 +31,7 @@ jobs:
           - 25.04.0
           - latest-everything
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
@@ -57,7 +57,7 @@ jobs:
 
   profile_test:
     runs-on: ubuntu-latest
-    name: Run ${{ matrix.profile }} profile
+    name: Run ${{ matrix.profile }} profile | ${{ matrix.NXF_VER }}
     needs: test_all_profiles
     strategy:
       fail-fast: false
@@ -215,15 +215,17 @@ jobs:
           - "wustl_htcf"
           - "xanadu"
           - "york_viking"
+        NXF_VER:
+          - "25.04.8"
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
         with:
           distribution: "temurin"
           java-version: "17"
       - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0
         with:
           version: "latest-everything"
       - name: Check ${{ matrix.profile }} profile

.github/workflows/update-pipeline-configs.yml

@@ -10,7 +10,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
       - name: Fetch pipeline names
         run: |
@@ -57,7 +57,7 @@ jobs:
           git commit -m "[automated] Update pipeline configs"
 
       - name: Create PR
-        uses: peter-evans/create-pull-request@70a41aba780001da0a30141984ae2a0c95d8704e # v6
+        uses: peter-evans/create-pull-request@c0f553fe549906ede9cf27b5156039d195d2ece0 # v8.1.0
         if: steps.check-pipelines.outputs.changed == 'true'
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -1,21 +1,29 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.15.0
     hooks:
-      - id: ruff # linter
+      - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
       - id: ruff-format # formatter
-
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        entry: prettier --experimental-cli --write --ignore-unknown --no-cache
+        additional_dependencies:
+          - prettier@3.8.1
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: end-of-file-fixer
 
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.2.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
 
   - repo: local
     hooks:

.prettierrc.yml

@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "**/*.{md,yml,yaml}"
+    options:
+      tabWidth: 2

CITATION.cff

@@ -1,32 +1,6 @@
 cff-version: 1.2.0
 message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
 authors:
-  - family-names: Ewels
-    given-names: Philip
-  - family-names: Peltzer
-    given-names: Alexander
-  - family-names: Fillinger
-    given-names: Sven
-  - family-names: Patel
-    given-names: Harshil
-  - family-names: Alneberg
-    given-names: Johannes
-  - family-names: Wilm
-    given-names: Andreas
-  - family-names: Ulysse Garcia
-    given-names: Maxime
-  - family-names: Di Tommaso
-    given-names: Paolo
-  - family-names: Nahnsen
-    given-names: Sven
-title: "The nf-core framework for community-curated bioinformatics pipelines."
-version: 2.4.1
-doi: 10.1038/s41587-020-0439-x
-date-released: 2022-05-16
-url: https://github.com/nf-core/tools
-prefered-citation:
-  type: article
-  authors:
     - family-names: Ewels
       given-names: Philip
     - family-names: Peltzer
@@ -45,12 +19,38 @@ prefered-citation:
       given-names: Paolo
     - family-names: Nahnsen
       given-names: Sven
-  doi: 10.1038/s41587-020-0439-x
-  journal: nature biotechnology
-  start: 276
-  end: 278
-  title: "The nf-core framework for community-curated bioinformatics pipelines."
-  issue: 3
-  volume: 38
-  year: 2020
-  url: https://dx.doi.org/10.1038/s41587-020-0439-x
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+    type: article
+    authors:
+        - family-names: Ewels
+          given-names: Philip
+        - family-names: Peltzer
+          given-names: Alexander
+        - family-names: Fillinger
+          given-names: Sven
+        - family-names: Patel
+          given-names: Harshil
+        - family-names: Alneberg
+          given-names: Johannes
+        - family-names: Wilm
+          given-names: Andreas
+        - family-names: Ulysse Garcia
+          given-names: Maxime
+        - family-names: Di Tommaso
+          given-names: Paolo
+        - family-names: Nahnsen
+          given-names: Sven
+    doi: 10.1038/s41587-020-0439-x
+    journal: nature biotechnology
+    start: 276
+    end: 278
+    title: "The nf-core framework for community-curated bioinformatics pipelines."
+    issue: 3
+    volume: 38
+    year: 2020
+    url: https://dx.doi.org/10.1038/s41587-020-0439-x

README.md

@@ -114,7 +114,6 @@ Within the local clone of your fork:
 2.  **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
 3.  **edit** and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone
 4.  **add** your profile name to GitHub Actions YAML `profile:` scope (under strategy matrix) in [`.github/workflows/main.yml`](.github/workflows/main.yml).
-
     - If you forget to do this the tests will fail with the error in GitHub Actions:
 
           ```bash

conf/daisybio.config

@@ -89,6 +89,3 @@ profiles {
         executor.queueSize = 5
     }
 }
-
-
-

conf/icr_alma.config

@@ -48,7 +48,3 @@ singularity {
     pullTimeout = 2.h
     cacheDir = '/data/scratch/shared/SINGULARITY-DOWNLOAD/nextflow/.singularity'
 }
-
-
-
-

conf/ki_luria.config

@@ -19,4 +19,3 @@ process {
     executor       = 'slurm'
     clusterOptions = '-p normal'
 }
-

conf/mssm.config

@@ -133,4 +133,3 @@ process {
     // Set default failOnMissingField behavior (optional)
     shell = ['/bin/bash', '-euo', 'pipefail']
 }
-

conf/tes.config

@@ -19,5 +19,3 @@ tes {
     basicUsername   = params.basicUsername
     basicPassword   = params.basicPassword
 }
-
-

conf/vsc_kul_uhasselt.config

@@ -316,5 +316,3 @@ profiles {
         }
     }
 }
-
-

docs/vsc_calcua.md

@@ -120,14 +120,12 @@ nextflow run nf-core/rnaseq \
 2.  Load Nextflow in your job script via the command: `module load Nextflow/23.04.2`. Alternatively, when using [your own version of Nextflow](#availability-of-nextflow), use `module load Java`.
 
 3.  Choose whether you want to use the [Slurm job scheduler to queue individual pipeline tasks](#schedule-nextflow-pipeline-using-slurm) (default mode) or if you prefer [local execution on a single node](#local-nextflow-run-on-a-single-interactive-node).
-
     - For Slurm scheduling, you only need to specify the `vsc_calcua` profile. E.g., `nextflow run pipeline -profile vsc_calcua`. Nextflow tasks will be scheduled as Slurm jobs to your current partition (or the one defined via `sbatch --partion=<partition-name>`).
     - For local execution mode on a single node, you need to append an additional sub-profile. E.g., `nextflow run pipeline -profile vsc_calcua,single_node`.
 
     Note that the `-profile` option can take multiple values, the first one always being `vsc_calcua` and the second `single_node` one being optional.
 
 4.  Specify the _partition_ that you want to run the pipeline on using the [`sbatch` command's `--partition=<name>` option](https://docs.vscentrum.be/jobs/job_submission.html#specifying-a-partition) and how many _resources_ should be allocated. See the [overview of partitions and their resources](#overview-of-partitions-and-resources) below, or refer to [the CalcUA documentation](https://docs.vscentrum.be/antwerp/tier2_hardware.html) for more info.
-
     - For the default Slurm scheduling, the partition on which the head process runs has no effect on the resources allocated to the actual pipeline tasks; these will instead be requested by Nextflow depending on the particular process' requirements and limited by the maximum thresholds set for each partition in this config.
     - For local execution mode on a single node, it is probably convenient to simply request a full node (e.g., `--cpus-per-task=28` and `--mem=112G` for broadwell), but if fewer resources are requested, these limits will be passed on the Nextflow too.
     - Omitting `--mem-per-cpu` or `--mem` will [allocate the default memory value](https://docs.vscentrum.be/jobs/job_submission.html#requesting-memory), which is the total available memory divided by the number of cores, e.g., `28 * 4 GB = 112 GB` for broadwell (`128 GB - 16 GB buffer`).