From e88c1673fd40632b1a8dee1dec66a737662afc3a Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 10:39:02 +0100 Subject: [PATCH 1/7] update/pin actions --- .github/workflows/fix-linting.yml | 14 +++++++------- .github/workflows/linting.yml | 6 +++--- .github/workflows/linting_comment.yml | 4 ++-- .github/workflows/main.yml | 10 +++++----- .github/workflows/update-pipeline-configs.yml | 4 ++-- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 2f1843890..092194e75 100644 --- a/.github/workflows/fix-linting.yml +++ b/.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 @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: 3.11 @@ -47,7 +47,7 @@ jobs: # 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 +67,21 @@ 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: | diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 34e8cb0fd..bfca5e7b1 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -16,6 +16,6 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 - - uses: pre-commit/action@v3.0.1 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 2f19378f0..c0a4a6476 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@5c98f0b039f36ef966fdb7dfa9779262785ecb05 # v14 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(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 }} diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 4c7b6764c..fc80bfd6b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -12,7 +12,7 @@ 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 @@ -20,7 +20,7 @@ jobs: runs-on: ubuntu-latest name: Check if nextflow config runs in repository root steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - name: Install Nextflow run: | wget -qO- get.nextflow.io | bash @@ -189,13 +189,13 @@ jobs: - "york_viking" 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 diff --git a/.github/workflows/update-pipeline-configs.yml b/.github/workflows/update-pipeline-configs.yml index 33515464c..00027071f 100644 --- a/.github/workflows/update-pipeline-configs.yml +++ b/.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 }} From bbdd3959aa4e4da73900224382dd1cfc369ec577 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 11:01:15 +0100 Subject: [PATCH 2/7] test default nextflow and (without failing) latest-everything for subset --- .github/workflows/main.yml | 30 ++++++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index fc80bfd6b..689b6ab69 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -29,9 +29,10 @@ 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 matrix: profile: - "abims" @@ -187,6 +188,30 @@ jobs: - "wustl_htcf" - "xanadu" - "york_viking" + NXF_VER: + - "25.04.8" + include: + # Test latest-everything with a representative subset of 10 profiles + - profile: "uppmax" + NXF_VER: "latest-everything" + - profile: "awsbatch" + NXF_VER: "latest-everything" + - profile: "googlebatch" + NXF_VER: "latest-everything" + - profile: "crick" + NXF_VER: "latest-everything" + - profile: "denbi_qbic" + NXF_VER: "latest-everything" + - profile: "pasteur" + NXF_VER: "latest-everything" + - profile: "phoenix" + NXF_VER: "latest-everything" + - profile: "jax" + NXF_VER: "latest-everything" + - profile: "imperial" + NXF_VER: "latest-everything" + - profile: "eddie" + NXF_VER: "latest-everything" steps: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 @@ -197,8 +222,9 @@ jobs: - name: Set up Nextflow uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2.0.0 with: - version: "latest-everything" + version: ${{ matrix.NXF_VER }} - name: Check ${{ matrix.profile }} profile + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: SCRATCH: "~" NXF_GLOBAL_CONFIG: awsbatch.config From 1ec2618a01a2a766977b30af036e5d7539f3da6c Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 13:51:51 +0100 Subject: [PATCH 3/7] drop testing latest-everything and add nextflow lint to pre-commit --- .github/workflows/main.yml | 23 ----------------------- .pre-commit-config.yaml | 5 +++++ 2 files changed, 5 insertions(+), 23 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 689b6ab69..ee8803015 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -190,28 +190,6 @@ jobs: - "york_viking" NXF_VER: - "25.04.8" - include: - # Test latest-everything with a representative subset of 10 profiles - - profile: "uppmax" - NXF_VER: "latest-everything" - - profile: "awsbatch" - NXF_VER: "latest-everything" - - profile: "googlebatch" - NXF_VER: "latest-everything" - - profile: "crick" - NXF_VER: "latest-everything" - - profile: "denbi_qbic" - NXF_VER: "latest-everything" - - profile: "pasteur" - NXF_VER: "latest-everything" - - profile: "phoenix" - NXF_VER: "latest-everything" - - profile: "jax" - NXF_VER: "latest-everything" - - profile: "imperial" - NXF_VER: "latest-everything" - - profile: "eddie" - NXF_VER: "latest-everything" steps: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 @@ -224,7 +202,6 @@ jobs: with: version: ${{ matrix.NXF_VER }} - name: Check ${{ matrix.profile }} profile - continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: SCRATCH: "~" NXF_GLOBAL_CONFIG: awsbatch.config diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index edf1bc116..e23449917 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,6 +16,11 @@ repos: hooks: - id: editorconfig-checker alias: ec + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.2.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' - repo: local hooks: From f786b1dbb37b606426070d18307eb418942e59db Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 13:52:54 +0100 Subject: [PATCH 4/7] update deps in pre-commit and replace editorconfig with pre-commit and prettier --- .editorconfig | 12 ------------ .pre-commit-config.yaml | 19 +++++++++++-------- .prettierrc.yml | 5 +++++ 3 files changed, 16 insertions(+), 20 deletions(-) delete mode 100644 .editorconfig diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 70c7a9a8e..000000000 --- a/.editorconfig +++ /dev/null @@ -1,12 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{md,yml,yaml,cff}] -indent_size = 2 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e23449917..8ee0d7111 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,24 @@ 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 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + 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: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + - id: end-of-file-fixer + - repo: https://github.com/seqeralabs/nf-lint-pre-commit rev: v0.2.0 hooks: diff --git a/.prettierrc.yml b/.prettierrc.yml index c81f9a766..5c313d490 100644 --- a/.prettierrc.yml +++ b/.prettierrc.yml @@ -1 +1,6 @@ printWidth: 120 +tabWidth: 4 +overrides: + - files: "**/*.{md,yml,yaml}" + options: + tabWidth: 2 From 1c17db21386b2c4e9b190cab53c693cb090969cc Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 13:57:14 +0100 Subject: [PATCH 5/7] switch to prek --- .github/workflows/fix-linting.yml | 9 +++++---- .github/workflows/linting.yml | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 092194e75..689999349 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,14 +34,15 @@ jobs: # Install and run pre-commit - 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 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfca5e7b1..30ef0e647 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -18,4 +18,4 @@ jobs: steps: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 + - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1 From 95fe69ef156fd1f9ddd80085fadead03abebacb2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 14:00:15 +0100 Subject: [PATCH 6/7] fix linting --- CITATION.cff | 70 ++++++++++++++++++------------------ README.md | 1 - conf/daisybio.config | 3 -- conf/embl_hd.config | 1 - conf/icr_alma.config | 4 --- conf/ki_luria.config | 1 - conf/mssm.config | 1 - conf/tes.config | 2 -- conf/vsc_kul_uhasselt.config | 2 -- docs/vsc_calcua.md | 2 -- 10 files changed, 35 insertions(+), 52 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 4533e2f28..db2ceba8b 100644 --- a/CITATION.cff +++ b/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 diff --git a/README.md b/README.md index e2ad2cb84..da8361209 100644 --- a/README.md +++ b/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 diff --git a/conf/daisybio.config b/conf/daisybio.config index d2b3ac715..b095460e7 100644 --- a/conf/daisybio.config +++ b/conf/daisybio.config @@ -76,6 +76,3 @@ profiles { } } - - - diff --git a/conf/embl_hd.config b/conf/embl_hd.config index 397b5a82f..567f75721 100644 --- a/conf/embl_hd.config +++ b/conf/embl_hd.config @@ -42,4 +42,3 @@ executor { exitReadTimeout = "5 min" retry.reason = "*" } - diff --git a/conf/icr_alma.config b/conf/icr_alma.config index 7ad5cec60..e0b04d702 100644 --- a/conf/icr_alma.config +++ b/conf/icr_alma.config @@ -48,7 +48,3 @@ singularity { pullTimeout = 2.h cacheDir = '/data/scratch/shared/SINGULARITY-DOWNLOAD/nextflow/.singularity' } - - - - diff --git a/conf/ki_luria.config b/conf/ki_luria.config index f7a96439c..625f5262f 100644 --- a/conf/ki_luria.config +++ b/conf/ki_luria.config @@ -19,4 +19,3 @@ process { executor = 'slurm' clusterOptions = '-p normal' } - diff --git a/conf/mssm.config b/conf/mssm.config index 127c8c292..6d1ba77c0 100644 --- a/conf/mssm.config +++ b/conf/mssm.config @@ -133,4 +133,3 @@ process { // Set default failOnMissingField behavior (optional) shell = ['/bin/bash', '-euo', 'pipefail'] } - diff --git a/conf/tes.config b/conf/tes.config index 88d44de1a..223b0cf6c 100644 --- a/conf/tes.config +++ b/conf/tes.config @@ -19,5 +19,3 @@ tes { basicUsername = params.basicUsername basicPassword = params.basicPassword } - - diff --git a/conf/vsc_kul_uhasselt.config b/conf/vsc_kul_uhasselt.config index 152e2028c..0d63ad806 100644 --- a/conf/vsc_kul_uhasselt.config +++ b/conf/vsc_kul_uhasselt.config @@ -316,5 +316,3 @@ profiles { } } } - - diff --git a/docs/vsc_calcua.md b/docs/vsc_calcua.md index 56f0af426..449f97192 100644 --- a/docs/vsc_calcua.md +++ b/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=`). - 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=` 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`). From 84570125c0265a0483e24da9eba836971c95ea44 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 13 Feb 2026 14:03:54 +0100 Subject: [PATCH 7/7] add setup-nextflow before the pre-commit step --- .github/workflows/fix-linting.yml | 3 +++ .github/workflows/linting.yml | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 689999349..57328cd4a 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -31,6 +31,9 @@ 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@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 30ef0e647..3e56f8239 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -17,5 +17,5 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 + - uses: nf-core/setup-nextflow@v2 - uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1.1.1