Merge branch 'main' of github.com:nf-core/tools into master-to-main

# Conflicts: # .github/RELEASE_CHECKLIST.md # .github/workflows/branch.yml # .github/workflows/pytest.yml # nf_core/pipeline-template/README.md # nf_core/pipeline-template/assets/schema_input.json # nf_core/pipeline-template/nextflow_schema.json
sanger-tol · Dec 3, 2024 · 73957fd · 73957fd
2 parents bd9608d + 41b4516
commit 73957fd
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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/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -9,15 +9,15 @@
 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 `main`
-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
@@ -53,6 +53,12 @@ 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
@@ -77,7 +83,7 @@ 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 main/master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `main/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: [main, master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo main/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 `main/master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,8 +32,8 @@ 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 }}) `main` branch.
-            The `main/master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `main/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.
+            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:
-          - "23.04.0"
+          - "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
@@ -40,11 +40,11 @@ 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: |
-          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
@@ -66,8 +66,6 @@ jobs:
             runner: ubuntu-latest
             profile: "docker"
         exclude:
-          - TEMPLATE: github
-          - TEMPLATE: is_nfcore
           - TEMPLATE: nf_core_configs
             profile: "self_hosted_runner"
       fail-fast: false
@@ -79,11 +77,11 @@ jobs:
           cd create-lint-wf-template
           export NXF_WORK=$(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"
 
@@ -139,6 +137,11 @@ 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' {} \;
@@ -149,6 +152,12 @@ jobs:
         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
@@ -165,7 +174,7 @@ 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:
-          - "23.04.0"
+          - "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