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Merge pull request #230 from nf-core/dev
Release 2.3.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
|
|
||
| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 | ||
| with: | ||
| 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." | ||
| 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." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: "${{ secrets.GITHUB_TOKEN }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
|
|
||
| # Run the workflow when: | ||
| # - dispatched manually | ||
| # - when a PR is opened or reopened to master branch | ||
| # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| testbranch: | ||
| description: "The specific branch you wish to utilize for the test execution of nf-core download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| branches: | ||
| - master | ||
| pull_request_target: | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| download: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | ||
|
|
||
| - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
| - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install git+https://github.com/nf-core/tools.git@dev | ||
| - name: Get the repository name and current branch set as environment variable | ||
| run: | | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} | ||
| echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} | ||
| - name: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| run: | | ||
| nf-core download ${{ env.REPO_LOWERCASE }} \ | ||
| --revision ${{ env.REPO_BRANCH }} \ | ||
| --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ | ||
| --compress "none" \ | ||
| --container-system 'singularity' \ | ||
| --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results |
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