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[wfpm v0.7.11] initial commit for argo-somatic-variant-calling project
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‎.github/workflows/build-test-release.yml‎

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name: CI/CD
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on:
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push:
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branches:
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- main
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- '*\@[0-9]+.[0-9]+.[0-9]+*' # package development branch
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jobs:
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build:
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if: ${{ !contains(github.event.head_commit.message, '[no ci]') }}
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runs-on: ubuntu-latest
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outputs:
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branch: ${{ steps.get_pkg_info.outputs.branch }}
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pkg_name: ${{ steps.get_pkg_info.outputs.pkg_name }}
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pkg_ver: ${{ steps.get_pkg_info.outputs.pkg_ver }}
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docker_file: ${{ steps.get_pkg_info.outputs.docker_file }}
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repo_lowercase: ${{ steps.repo_lowercase.outputs.lowercase }}
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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- name: Extract package name and version from branch name
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id: get_pkg_info
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shell: bash
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run: |
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echo "::set-output name=branch::$(echo ${GITHUB_REF#refs/heads/})"
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PKG_NAME=$(echo ${GITHUB_REF#refs/heads/} | awk -F'@' '{print $1}')
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PKG_VER=$(echo ${GITHUB_REF#refs/heads/} | awk -F'@' '{print $2}')
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echo "::set-output name=pkg_name::$(echo $PKG_NAME)"
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echo "::set-output name=pkg_ver::$(echo $PKG_VER)"
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if [[ -f "./$PKG_NAME/Dockerfile" ]]; then
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echo "::set-output name=docker_file::$(echo ./$PKG_NAME/Dockerfile)"
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else
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echo "::set-output name=docker_file::"
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fi
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- name: Login to GitHub Container Registry
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if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}}
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uses: docker/login-action@v1
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.CR_PAT }}
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- id: repo_lowercase
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uses: ASzc/change-string-case-action@v1
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with:
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string: ${{ github.repository }}
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- name: Build image
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if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}}
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uses: docker/build-push-action@v2
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with:
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context: "./${{steps.get_pkg_info.outputs.pkg_name}}"
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file: "${{steps.get_pkg_info.outputs.docker_file}}"
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platforms: linux/amd64
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load: true
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tags: |
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ghcr.io/${{ steps.repo_lowercase.outputs.lowercase }}.${{ steps.get_pkg_info.outputs.pkg_name }}:${{ steps.get_pkg_info.outputs.pkg_ver }}
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- name: Push image to ghcr.io
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id: push_to_ghcr
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if: ${{ steps.get_pkg_info.outputs.branch != 'main' && steps.get_pkg_info.outputs.docker_file != ''}}
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shell: bash
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run: |
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docker push ghcr.io/${{ steps.repo_lowercase.outputs.lowercase }}.${{ steps.get_pkg_info.outputs.pkg_name }}:${{ steps.get_pkg_info.outputs.pkg_ver }} | tee ./ghcr.io.stdout
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IMAGE_SHA=$(cat ./ghcr.io.stdout | tr ' ' '\n' | grep 'sha256:' | awk -F':' '{print $2}')
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echo "::set-output name=image_sha256::$(echo ${IMAGE_SHA})"
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echo "::set-output name=created_at::$(date -u +%FT%TZ)"
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test-and-release:
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runs-on: ubuntu-latest
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needs: [build]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.6
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uses: actions/setup-python@v2
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with:
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python-version: 3.6
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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 wfpm
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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if [ -f requirements-test.txt ]; then pip install -r requirements-test.txt; fi
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if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
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- name: Install Nextflow
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run: |
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wget --tries=10 -qO- https://get.nextflow.io | bash
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sudo chmod 755 nextflow
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sudo mv nextflow /usr/local/bin/
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- name: "Login to GitHub Container Registry" # normally shouldn't need to login, but new image when just created is private
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uses: docker/login-action@v1
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with:
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registry: ghcr.io
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username: ${{ github.repository_owner }}
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password: ${{ secrets.CR_PAT }}
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- name: Run tests for all packages
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if: ${{ needs.build.outputs.branch == 'main' }}
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run: |
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wfpm test
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- name: Run tests for the current package only
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if: ${{ needs.build.outputs.branch != 'main' }}
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run: |
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cd ./${{needs.build.outputs.pkg_name}}
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wfpm test
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- name: Check whether to proceed with release
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id: to_release
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run: |
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if [[ \
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"${{ github.event.head_commit.message }}" = "Merge"[[:space:]]"pull"[[:space:]]"request"* && \
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"${{ github.event.head_commit.message }}" = *"@"* && \
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"${{ github.event.head_commit.message }}" = *"[release]"* && \
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"${{ needs.build.outputs.branch }}" = 'main'
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]]; then
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echo "::set-output name=release::$(echo Y)"
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else
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echo "::set-output name=release::$(echo N)"
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fi
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- name: Extract package name and version from commit message
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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id: get_pkg_info
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shell: bash
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run: |
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MERGED_BR=$(echo -e '${{ github.event.head_commit.message }}' | \
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{ grep '^Merge pull request'||:; } | tr ' ' '\n' |{ grep '@'||:; } | awk -F'/' '{print $2}')
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PKG_NAME=$(echo $MERGED_BR | awk -F'@' '{print $1}')
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PKG_VER=$(echo $MERGED_BR | awk -F'@' '{print $2}')
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echo "::set-output name=pkg_name::$(echo ${PKG_NAME})"
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echo "::set-output name=pkg_ver::$(echo ${PKG_VER})"
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if [[ -f "./$PKG_NAME/Dockerfile" ]]; then
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echo "::set-output name=docker_file::$(echo ./$PKG_NAME/Dockerfile)"
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echo "::set-output name=docker_image::$(echo ghcr.io/${{ needs.build.outputs.repo_lowercase }}.$PKG_NAME:$PKG_VER)"
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else
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echo "::set-output name=docker_file::"
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echo "::set-output name=docker_image::"
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fi
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- name: Prepare package release tarball
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id: prep_assets
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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shell: bash
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run: |
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./scripts/cleanup_temp_files.sh # just in case
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PKG_TAR=${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}.tar.gz
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pushd ${{ steps.get_pkg_info.outputs.pkg_name }}
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tar --exclude=wfpr_modules --dereference -czvf ../$PKG_TAR .
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popd
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echo "::set-output name=pkg_tar::$(echo ${PKG_TAR})"
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echo "::set-output name=pkg_tar_sha::$(sha256sum ${PKG_TAR} |awk '{print $1}')"
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echo "::set-output name=pkg_tar_size::$(ls -l ${PKG_TAR} |awk '{print $5}')"
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echo "::set-output name=created_at::$(date -u +%FT%TZ)"
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- name: Create release
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id: create_release
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}
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release_name: ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}
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body: |
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* Release `${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}` (${{ github.sha }})
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* Package `${{ steps.prep_assets.outputs.pkg_tar }}` (sha256: `${{ steps.prep_assets.outputs.pkg_tar_sha }}`)
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* Package URI `github.com/${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}@${{ steps.get_pkg_info.outputs.pkg_ver }}`
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* Run the package: `nextflow run ${{ needs.build.outputs.repo_lowercase }}/${{ steps.get_pkg_info.outputs.pkg_name }}/main.nf -r ${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }} -params-file <params-json-file>`
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draft: false
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prerelease: false
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- name: Prepare in pkg-release.json
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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shell: bash
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run: |
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WFPM_VER=$(wfpm -v | cut -d ' ' -f 2)
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if [[ '${{ steps.get_pkg_info.outputs.docker_file }}' != '' ]]; then
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docker pull ${{ steps.get_pkg_info.outputs.docker_image }} | tee image.info
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IMAGE_SHA=$(cat ./image.info | tr ' ' '\n' | grep 'sha256:' | awk -F':' '{print $2}')
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else
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IMAGE_SHA=$(echo)
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fi
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# temporary solution
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TAG="${{ steps.get_pkg_info.outputs.pkg_name }}.v${{ steps.get_pkg_info.outputs.pkg_ver }}"
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./scripts/prepare_package_release_json.py -p ${{ steps.get_pkg_info.outputs.pkg_name }}/pkg.json -d \
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"
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{
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\"_release\": {
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\"created\": \"${{ steps.prep_assets.outputs.created_at }}\",
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\"hash\": {
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\"checksum_type\": \"sha1\",
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\"checksume\": \"${{ github.sha }}\"
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},
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\"tag\": \"$TAG\",
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\"assets\": [
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{
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\"filename\": \"$TAG.tar.gz\",
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\"download_url\": \"https://github.com/${{ github.repository }}/releases/download/$TAG/$TAG.tar.gz\",
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\"checksum\": \"${{ steps.prep_assets.outputs.pkg_tar_sha }}\",
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\"checksum_type\": \"sha256\",
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\"size\": ${{ steps.prep_assets.outputs.pkg_tar_size }}
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},
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{
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\"_NOTE_\": \"this file\",
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\"filename\": \"pkg-release.json\",
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\"download_url\": \"https://github.com/${{ github.repository }}/releases/download/$TAG/pkg-release.json\",
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\"checksum\": null,
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\"checksum_type\": null,
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\"size\": null
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}
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]
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},
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\"_image_digest\": {
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\"checksum\": \"$IMAGE_SHA\",
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\"checksum_type\": \"sha256\"
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},
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\"_wfpm_ver\": \"$WFPM_VER\"
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}
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" > pkg-release.json
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- name: Upload package release tarball
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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asset_path: ./${{ steps.prep_assets.outputs.pkg_tar }}
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asset_name: ${{ steps.prep_assets.outputs.pkg_tar }}
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asset_content_type: application/zip
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- name: Upload package release json
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if: ${{ steps.to_release.outputs.release == 'Y' }}
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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asset_path: ./pkg-release.json
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asset_name: pkg-release.json
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asset_content_type: application/json

‎.gitignore‎

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*.py[cod]
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# C extensions
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*.so
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# Packages
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*.egg
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*.egg-info
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dist
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build
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eggs
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.eggs
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parts
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bin
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var
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sdist
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develop-eggs
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.installed.cfg
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lib
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lib64
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venv*/
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pyvenv*/
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# Installer logs
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pip-log.txt
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# Unit test / coverage reports
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.coverage
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.tox
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.coverage.*
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nosetests.xml
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coverage.xml
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htmlcov
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# Translations
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*.mo
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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.idea
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*.iml
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*.komodoproject
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# Complexity
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output/*.html
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output/*/index.html
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# Sphinx
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docs/_build
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.DS_Store
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*~
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.*.sw[po]
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.build
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.ve
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.env
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.cache
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.pytest
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.bootstrap
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.appveyor.token
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*.bak
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*.log
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.vscode
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.python-version
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.nextflow*
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work
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outdir
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wfpr_modules/github.com/*/*/*/tests
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# singularity images
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**/*.img
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**/*.sif

‎.wfpm‎

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project_name: argo-somatic-variant-calling
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license: MIT
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repo_type: git
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repo_server: github.com
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repo_account: icgc-argo-workflows

‎LICENSE‎

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MIT License
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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎LICENSE-short‎

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Copyright (c) 2021, ICGC ARGO
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# A collection of somatic variant callers
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Update this to describe your awesome project.

‎nextflow.config‎

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manifest {
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homePage = 'https://github.com/icgc-argo-workflows/argo-somatic-variant-calling'
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description = 'A collection of somatic variant callers'
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nextflowVersion = '>=20.10'
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}
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docker {
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enabled = true
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runOptions = '-u \$(id -u):\$(id -g)'
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}

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