Merge dev third rev (#20)

* write only relevant fields in `.nf-core.yml` * switch from docstrings to Field descsriptions * [automated] Update CHANGELOG.md * update test to new error * second attempt to add ro crates * fix import * first running version * restructure code and add tests * add missing dep * add recommendations from comments * add git contributors * fix filename for CI * better help hint message * fix class name * add correct parent directory to faked crate * add empty ro-crate after sync * fix tests * fix ci test * use github to guess author name, set names as ids if no orcid * add bioschemas, datecreated and datemodified (only set to current time atm) * follow `ComputationalWorkflow` schema for main entitty. * fix date created field * add "about" field to workflow diagram * add input as separate entity * add version to main entity * fix incorrect type * switch to add_workflow method to add main entity and add components as datasets with descriptions * ro_crate -> rocrate * allow mixed list and dict in lint config * nested too deeply * [automated] Update CHANGELOG.md * use repo2crate to generate the main structure of the crate * chore(deps): update dependency prompt_toolkit to <=3.0.48 * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 * chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * Fix typos * Fix typos (second round) * Undo accidental typos fixes * Fix typos (third round) * Update textual snapshots * chore(deps): update python:3.12-slim docker digest to 032c526 * [automated] Update CHANGELOG.md * handle new nf-core.yml structure * update documentation for `multiqc_config` linting * parse yaml correctly * found a better way to handle the ignore file being None * handle new lint config structure * add tests with different valid yaml structures * use correct profile options for sfw test command * [automated] Update CHANGELOG.md * remove last traces of LintConfigType * fix incorrect type * more type fixes * Update CHANGELOG.md * add all lint tests to config * switch all defaults to None and drop them on dump * Update nf_core/utils.py Co-authored-by: Júlia Mir Pedrol <[email protected]> * Update nf_core/utils.py * drop None values when checking for test names * [automated] Fix code linting * no need for Field value * fix test_lint tests * fix worklfow_dispatch trigger and parse more review comments * [automated] Update CHANGELOG.md * Update pre-commit hook pre-commit/mirrors-mypy to v1.13.0 * chore(deps): update github actions * [automated] Update CHANGELOG.md * remove outdated file * Revert "Add new command `nf-core rocrate` to create a Research Object (RO) crate for a pipeline" * move test in correct directory * fix tests * Add seqera containers example * bump ci * Modify test_find_container_images_modules() for Seqera Containers. * Enable Seqera Containers download. * run tests without commiting ro-crate * add ro-crate creation to pipelines create command * fix command import * add rocrate to skip features * remove schema loading, because it is not needed anymore * update snapshots * `modules update`: add a panel around diffs * add `--dir/-d` option to schema commands * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * try to fix coverage report generation * fix test_cli * nf-core download: Fix forgotten symlinks in cache. * try specifying the coverage output file * try naming the files directly * fix variable name * add hiddnen files for upload-artifact action v4 * group diffs by module * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 * [automated] Update CHANGELOG.md * Update GitHub Actions * Ensure that prioritize_direct_download() retains Seqera Singularity Containers and write additional test. * make group border blue * make module names white * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <[email protected]> * Add resource limits to Gitpod profile * Update changelog * I fix typos for infrastickers * Fix typo * Update changelog * Update Gitpod to use Miniforge instead of Miniconda * Update Changelog * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 * [automated] Update CHANGELOG.md * handle new schema structure in create-params-file * add tests * [automated] Update CHANGELOG.md * add hint to solve git errors with a synced repo * run pre-commit when testing linting the template pipeline * [automated] Update CHANGELOG.md * [automated] Update CHANGELOG.md * fix template trailing spaces * write proper path and raise a UserWarning to avoid printing the error trace * Apply suggestions from code review Co-authored-by: Matthias Hörtenhuber <[email protected]> * remove logging git error from wrong place * add option to skip .vscode from the template * update textual snapshots * update and fix swf patch tests * Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 * [automated] Update CHANGELOG.md * Update codecov/codecov-action action to v5 (nf-core#3283) * Update codecov/codecov-action action to v5 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * Update python:3.12-slim Docker digest to 2a6386a (nf-core#3284) * Update python:3.12-slim Docker digest to 2a6386a * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * apply patch reverse when linting a patched subworkflow * update get_patch_fn to work with subworkflows * move modules_differ.py to components_differ.py * add subworkflows patch missing tests * fix subworkflows update test * update changelog * add help text for --remove flag * apply code review suggestions to patch tests * Update tests/modules/test_patch.py * apply suggestions by @mashehu * remove def from nextflow.config and add trace_report_suffix param * [automated] Update CHANGELOG.md * Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 * [automated] Update CHANGELOG.md * add validation.monochromeLogs to config * ignore trace_report_suffix default check * update snapshots * add more tests * enable zip output * Move modules config import after base.config * Update nf_core/pipelines/create/template_features.yml * Update documentation * Update CHANGELOG * Update CHANGELOG.md * Fix linting * Update CHANGELOG * Download: Need to deduplicate Seqera Container matches as well, otherwise a race condition emerges. * Add new function to handle Seqera Container Oras URIs. * Ensure, that oras:// containers are correctly handled. * Download: Add test data for oras:// modules. * Test the new container elimination routine. * Download: Update the tests. * Add dedicated ORAS image format error. * Include oras:// regex in download to recognize the paths. * Changelog. * Update dawidd6/action-download-artifact action to v7 (nf-core#3306) * Update dawidd6/action-download-artifact action to v7 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.1 * Update gitpod/workspace-base Docker digest to 12853f7 (nf-core#3309) * Update gitpod/workspace-base Docker digest to 12853f7 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> * update modules and subworkflows * [automated] Update CHANGELOG.md * also add monochrome_logs if nf-schema is used * add manifest.contributors to nextflow.config * [automated] Update CHANGELOG.md * fix contributors map * Update nf_core/pipeline-template/.github/CONTRIBUTING.md Co-authored-by: Phil Ewels <[email protected]> * Typo in error message. Co-authored-by: Matthias Hörtenhuber <[email protected]> * test also the main sync function itsel * combine json parsing code * loop over list of authors to supply contributors * remove broken test * fix type error * Apply suggestions from code review Co-authored-by: Júlia Mir Pedrol <[email protected]> --------- Co-authored-by: mashehu <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]> Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Phil Ewels <[email protected]> Co-authored-by: Louis LE NEZET <[email protected]> Co-authored-by: Louis Le Nezet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]>
sanger-tol · Dec 4, 2024 · c0b51d7 · c0b51d7
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diff --git a/.github/.coveragerc b/.github/.coveragerc
@@ -2,4 +2,3 @@
 omit = nf_core/*-template/*
 source = nf_core
 relative_files = True
-
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -6,7 +6,7 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a release.
 
-Learn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md
+Learn more about contributing: https://github.com/nf-core/tools/tree/main/.github/CONTRIBUTING.md
 -->
 
 ## PR checklist

diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -6,18 +6,18 @@
 4. Check that modules/subworkflows in template are up to date with the latest releases
 5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
-7. Create a PR from `dev` to `master`
-8. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
+7. Create a PR from `dev` to `main`
+8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
 9. Request review (2 approvals required)
-10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
-11. Merge the PR into `master`
-12. Wait for CI tests on the commit to passed
-13. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
-14. Create a new release copying the `CHANGELOG` for that release into the description section.
+10. Merge the PR into `main`
+11. Wait for CI tests on the commit to passed
+12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+13. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 
 1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template.
 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
 4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.
+5. Run `rich-codex` on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml) to regenerate docs screengrabs (actions `workflow_dispatch` button)
diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
@@ -53,12 +53,24 @@ runs:
       run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
       working-directory: create-lint-wf
 
+    # Uncomment includeConfig statement
+    - name: uncomment include config
+      shell: bash
+      run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
+      working-directory: create-lint-wf
+
     # Replace zenodo.XXXXXX to pass readme linting
     - name: replace zenodo.XXXXXX
       shell: bash
       run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
+    # Add empty ro-crate file
+    - name: add empty ro-crate file
+      shell: bash
+      run: touch nf-core-testpipeline/ro-crate-metadata.json
+      working-directory: create-lint-wf
+
     # Run nf-core pipelines linting
     - name: nf-core pipelines lint
       shell: bash
@@ -77,7 +89,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+      uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
@@ -21,7 +21,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -31,9 +31,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir
@@ -48,12 +48,12 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: pip
@@ -78,6 +78,11 @@ jobs:
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
         working-directory: create-lint-wf
 
+      # Uncomment includeConfig statement
+      - name: uncomment include config
+        run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
+        working-directory: create-lint-wf
+
       # Run the other nf-core commands
       - name: nf-core pipelines list
         run: nf-core --log-file log.txt pipelines list

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -40,7 +40,7 @@ jobs:
       - name: 🏗 Set up yq
         uses: frenck/action-setup-yq@v1
       - name: checkout
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -77,11 +77,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -137,16 +137,32 @@ jobs:
         run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
         working-directory: create-test-lint-wf
 
+      # Uncomment includeConfig statement
+      - name: uncomment include config
+        run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
+        working-directory: create-test-lint-wf
+
       # Replace zenodo.XXXXXX to pass readme linting
       - name: replace zenodo.XXXXXX
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
         working-directory: create-test-lint-wf
 
+      # Add empty ro-crate file
+      - name: add empty ro-crate file
+        run: touch my-prefix-testpipeline/ro-crate-metadata.json
+        working-directory: create-test-lint-wf
+
       # Run nf-core linting
       - name: nf-core pipelines lint
         run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned
         working-directory: create-test-lint-wf
 
+      # Run code style linting
+      - name: run pre-commit
+        shell: bash
+        run: pre-commit run --all-files
+        working-directory: create-test-lint-wf
+
       # Run bump-version
       - name: nf-core pipelines bump-version
         run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1
@@ -163,7 +179,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.10.0"
+          - "24.04.2"
           - "latest-everything"
     steps:
       - name: go to working directory
@@ -48,11 +48,11 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -71,15 +71,11 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          # echo current directory
-          pwd
-          # echo content of current directory
-          ls -la
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
+          nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

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@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,10 +18,10 @@ jobs:
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           cache: "pip"

diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,3 @@
		omit = nf_core/-template/
		source = nf_core
		relative_files = True