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Merge pull request #443 from nf-core/dev
Patch release: 1.1.5
2 parents 21e6af8 + 8018d50 commit 9f47401

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‎.devcontainer/devcontainer.json

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@@ -18,11 +18,11 @@
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"python.linting.flake8Path": "/opt/conda/bin/flake8",
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"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
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"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
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"python.linting.pylintPath": "/opt/conda/bin/pylint",
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
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},
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},
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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}
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}

‎.editorconfig

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@@ -22,3 +22,11 @@ indent_size = unset
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[/assets/email*]
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indent_size = unset
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# ignore Readme
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[README.md]
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indent_style = unset
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# ignore python
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[*.{py}]
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indent_style = unset

‎.github/workflows/awsfulltest.yml

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}
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profiles: test_full
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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path: |

‎.github/workflows/awstest.yml

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@@ -25,7 +25,7 @@ jobs:
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}
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profiles: test
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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path: |

‎.github/workflows/branch.yml

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@@ -19,7 +19,7 @@ jobs:
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@v1
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uses: mshick/add-pr-comment@v2
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with:
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message: |
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## This PR is against the `master` branch :x:

‎.github/workflows/ci.yml

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@@ -59,12 +59,12 @@ jobs:
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- name: Run pipeline with test data
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run: |
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if [[ "${{ matrix.tags }}" == "test_motus" ]]; then
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wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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if [[ "${{ matrix.tags }}" == "test_motus" ]]; then
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wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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python downloadDB.py > download_db_log.txt
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echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
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echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
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nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }};
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else
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nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }};
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else
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nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --outdir ./results_${{ matrix.tags }};
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fi

‎.github/workflows/clean-up.yml

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@@ -10,7 +10,7 @@ jobs:
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issues: write
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pull-requests: write
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steps:
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- uses: actions/stale@v7
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- uses: actions/stale@v9
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with:
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stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
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stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

‎.github/workflows/download_pipeline.yml

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@@ -0,0 +1,67 @@
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name: Test successful pipeline download with 'nf-core download'
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# Run the workflow when:
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# - dispatched manually
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# - when a PR is opened or reopened to master branch
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# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
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on:
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workflow_dispatch:
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pull_request:
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types:
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- opened
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branches:
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- master
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pull_request_target:
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branches:
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- master
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env:
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NXF_ANSI_LOG: false
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jobs:
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download:
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runs-on: ubuntu-latest
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steps:
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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- uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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architecture: "x64"
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- uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.3
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install git+https://github.com/nf-core/tools.git@dev
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- name: Get the repository name and current branch set as environment variable
42+
run: |
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echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
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echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
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echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
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- name: Download the pipeline
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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run: |
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nf-core download ${{ env.REPO_LOWERCASE }} \
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--revision ${{ env.REPO_BRANCH }} \
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--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
54+
--compress "none" \
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--container-system 'singularity' \
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--container-library "quay.io" -l "docker.io" -l "ghcr.io" \
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--container-cache-utilisation 'amend' \
58+
--download-configuration
59+
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- name: Inspect download
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run: tree ./${{ env.REPOTITLE_LOWERCASE }}
62+
63+
- name: Run the downloaded pipeline
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env:
65+
NXF_SINGULARITY_CACHEDIR: ./
66+
NXF_SINGULARITY_HOME_MOUNT: true
67+
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

‎.github/workflows/fix-linting.yml

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@@ -4,7 +4,7 @@ on:
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types: [created]
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jobs:
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deploy:
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fix-linting:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
@@ -13,43 +13,77 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
16-
- uses: actions/checkout@v4
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# indication that the linting is being fixed
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- name: React on comment
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: eyes
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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27-
- uses: actions/setup-node@v4
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# Install and run pre-commit
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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with:
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python-version: 3.11
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- name: Install Prettier
30-
run: npm install -g prettier @prettier/plugin-php
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- name: Install pre-commit
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run: pip install pre-commit
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# Check that we actually need to fix something
33-
- name: Run 'prettier --check'
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
37-
echo "result=pass" >> $GITHUB_OUTPUT
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else
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echo "result=fail" >> $GITHUB_OUTPUT
40-
fi
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- name: Run pre-commit
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id: pre-commit
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run: pre-commit run --all-files
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continue-on-error: true
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- name: Run 'prettier --write'
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if: steps.prettier_status.outputs.result == 'fail'
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run: prettier --write ${GITHUB_WORKSPACE}
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# indication that the linting has finished
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- name: react if linting finished succesfully
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if: steps.pre-commit.outcome == 'success'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: "+1"
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- name: Commit & push changes
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if: steps.prettier_status.outputs.result == 'fail'
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id: commit-and-push
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if: steps.pre-commit.outcome == 'failure'
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run: |
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git config user.email "[email protected]"
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git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix linting with Prettier"
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git commit -m "[automated] Fix code linting"
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git push
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67+
- name: react if linting errors were fixed
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id: react-if-fixed
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if: steps.commit-and-push.outcome == 'success'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
72+
comment-id: ${{ github.event.comment.id }}
73+
reactions: hooray
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- name: react if linting errors were not fixed
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if: steps.commit-and-push.outcome == 'failure'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
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comment-id: ${{ github.event.comment.id }}
80+
reactions: confused
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- name: react if linting errors were not fixed
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if: steps.commit-and-push.outcome == 'failure'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
86+
issue-number: ${{ github.event.issue.number }}
87+
body: |
88+
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
89+
See [CI log](https://github.com/nf-core/taxprofiler/actions/runs/${{ github.run_id }}) for more details.

‎.github/workflows/linting.yml

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types: [published]
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jobs:
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EditorConfig:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v4
20-
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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- name: Run ECLint check
25-
run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
26-
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Prettier:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v4
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- name: Install Prettier
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run: npm install -g prettier
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- name: Run Prettier --check
38-
run: prettier --check ${GITHUB_WORKSPACE}
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PythonBlack:
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runs-on: ubuntu-latest
42-
steps:
43-
- uses: actions/checkout@v4
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45-
- name: Check code lints with Black
46-
uses: psf/black@stable
47-
48-
# If the above check failed, post a comment on the PR explaining the failure
49-
- name: Post PR comment
50-
if: failure()
51-
uses: mshick/add-pr-comment@v1
19+
- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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message: |
54-
## Python linting (`black`) is failing
55-
56-
To keep the code consistent with lots of contributors, we run automated code consistency checks.
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To fix this CI test, please run:
58-
59-
* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
60-
* Fix formatting errors in your pipeline: `black .`
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62-
Once you push these changes the test should pass, and you can hide this comment :+1:
22+
python-version: 3.11
23+
cache: "pip"
6324

64-
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
25+
- name: Install pre-commit
26+
run: pip install pre-commit
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66-
Thanks again for your contribution!
67-
repo-token: ${{ secrets.GITHUB_TOKEN }}
68-
allow-repeats: false
28+
- name: Run pre-commit
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run: pre-commit run --all-files
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nf-core:
7132
runs-on: ubuntu-latest
@@ -76,7 +37,7 @@ jobs:
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- name: Install Nextflow
7738
uses: nf-core/setup-nextflow@v1
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- uses: actions/setup-python@v4
40+
- uses: actions/setup-python@v5
8041
with:
8142
python-version: "3.11"
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architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
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10061
- name: Upload linting log file artifact
10162
if: ${{ always() }}
102-
uses: actions/upload-artifact@v3
63+
uses: actions/upload-artifact@v4
10364
with:
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name: linting-logs
10566
path: |

‎.github/workflows/linting_comment.yml

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runs-on: ubuntu-latest
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steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@v2
14+
uses: dawidd6/action-download-artifact@v3
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with:
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workflow: linting.yml
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@v4
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- uses: actions/setup-python@v5
2828
with:
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python-version: "3.10"
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- name: Install dependencies
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bsky-post:
5757
runs-on: ubuntu-latest
5858
steps:
59-
- uses: zentered/bluesky-post-action@v0.0.2
59+
- uses: zentered/bluesky-post-action@v0.1.0
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with:
6161
post: |
6262
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

‎.gitpod.yml

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- name: unset JAVA_TOOL_OPTIONS
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command: |
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unset JAVA_TOOL_OPTIONS
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1011
vscode:
1112
extensions: # based on nf-core.nf-core-extensionpack
1213
- codezombiech.gitignore # Language support for .gitignore files

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v2.7.1"
3+
rev: "v3.1.0"
44
hooks:
55
- id: prettier
6+
- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
7+
rev: "2.7.3"
8+
hooks:
9+
- id: editorconfig-checker
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alias: ec

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