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remove everything but the bam file in Fetch_SRA_to_BAM #2415

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remove everything but the bam file in Fetch_SRA_to_BAM

remove everything but the bam file in Fetch_SRA_to_BAM #2415

Workflow file for this run

.github/workflows/build.yml at 255271a
name: "viral-pipelines CI"
on:
push:
merge_group:
pull_request:
branches:
- master
release:
types:
- created
env:
PYTHONIOENCODING: UTF8
DOCKER_REGISTRY: "quay.io"
DOCKER_REPO_PROD: "quay.io/broadinstitute/viral-pipelines"
DOCKER_REPO_DEV: "quay.io/broadinstitute/viral-pipelines-dev"
MODULE_VERSIONS: "requirements-modules.txt"
# TravisCI variables described here:
# https://docs.travis-ci.com/user/environment-variables/
# GitHub Actions environment variables and context described here:
# https://docs.github.com/en/actions/reference/environment-variables
# https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#env-context
GITHUB_ACTIONS_COMMIT: ${{ github.sha }}
GITHUB_ACTIONS_BUILD_DIR: ${{ github.workspace }}
GITHUB_ACTIONS_BRANCH: ${{ github.ref }}
GITHUB_ACTIONS_PULL_REQUEST: ${{ github.event.number }}
GITHUB_ACTIONS_PULL_REQUEST_BRANCH: ${{ github.head_ref }}
GITHUB_ACTIONS_PULL_REQUEST_SHA : ${{ github.event.pull_request.head.sha }}
GITHUB_ACTIONS_BASE_REF: ${{ github.base_ref }}
jobs:
validate_wdl_miniwdl:
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
# if GITHUB_ACTIONS_PULL_REQUEST_BRANCH is set, this is a pull request build
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: List environment
run: |
env
- name: install python
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: install system dependencies
run: |
sudo apt-get update
sudo apt-get -y install shellcheck
- name: install miniwdl
run: |
pip3 -q install miniwdl
- name: run miniwdl checks
shell: bash
run: |
set -e
github_actions_ci/check-wdl-runtimes.sh
miniwdl check pipes/WDL/workflows/*.wdl
validate_wdl_womtool:
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: install java
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '11'
- name: install cromwell+womtool+dxWDL
shell: bash
run: |
github_actions_ci/install-wdl.sh
- name: run womtool checks
shell: bash
run: |
set -e
github_actions_ci/check-wdl-runtimes.sh
github_actions_ci/validate-wdl-womtool.sh
## note: this test_docs job does not actually produce the output on readthedocs
## readthedocs does its own build trigger. this job exists simply to
## attempt a build and alert us of documentation build failures because otherwise we would never know.
test_docs:
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: install python
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: install docs dependencies
shell: bash
run: |
github_actions_ci/install-pip-docs.sh
- name: test docs build
shell: bash
run: |
github_actions_ci/build-docs.sh
test_cromwell:
needs: validate_wdl_womtool
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: clean up disk space
shell: bash
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install java
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '11'
- name: install cromwell+womtool+dxWDL
shell: bash
run: |
github_actions_ci/install-wdl.sh
- name: test with cromwell
shell: bash
run: |
set -e
github_actions_ci/relative-wdl-paths.sh
github_actions_ci/tests-cromwell.sh
test_miniwdl:
needs: validate_wdl_miniwdl
runs-on: ubuntu-20.04
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: clean up disk space
shell: bash
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install python
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: install system dependencies
run: |
sudo apt-get update
sudo apt-get -y install jq
- name: install miniwdl
run: |
pip3 install miniwdl docker[tls] six
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: test with miniwdl
shell: bash
run: |
github_actions_ci/tests-miniwdl.sh
deploy_dnanexus:
#if: ${{ github.event.ref == 'dnanexus' }}
if: github.event_name == 'release' || github.ref == 'refs/heads/master' || github.ref == 'refs/heads/dnanexus'
needs:
- validate_wdl_womtool
- validate_wdl_miniwdl
runs-on: ubuntu-20.04
env:
# DX_API_TOKEN (for DNAnexus builds) -- GitHub Actions token #1, expires 2025-01-17
# stored here: https://github.com/broadinstitute/viral-pipelines/settings/secrets/actions
DX_API_TOKEN: ${{ secrets.DX_API_TOKEN }}
DX_PROJECT: project-F8PQ6380xf5bK0Qk0YPjB17P
steps:
- name: checkout repository
uses: actions/checkout@v4
# fetch git tags (tagged releases) because
# actions/checkout@v4 does either a full checkout or a shallow checkout without tags
- name: fetch tags
run: git fetch --prune --unshallow --tags
- name: Programmatic environment setup
run: |
set -e -x
# $GITHUB_ENV is available for subsequent steps
GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '')
echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV
#
# Set GITHUB_ACTIONS_BRANCH
# TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ )
# for push builds, or builds not triggered by a pull request, this is the name of the branch.
# for builds triggered by a pull request this is the name of the branch targeted by the pull request.
# for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG).
if [[ $GITHUB_ACTIONS_PULL_REQUEST_BRANCH ]]; then
GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/}
# if event_name=="release", this is a tagged build
elif [[ "${{ github.event_name }}" == "release" ]]; then
GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG
else
GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: list GH event info
run: |
echo "${{ github.event_name }}"
echo "${{ github.event.action }}"
echo "${{ github.event.pull_request.merged }}"
- name: install python
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: install java
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '11'
- name: install miniwdl
run: |
pip3 install pyyaml dxpy
- name: install dx toolkit
shell: bash
run: |
github_actions_ci/install-wdl.sh
- name:
shell: bash
run: |
github_actions_ci/relative-wdl-paths.sh
github_actions_ci/build-dx.sh
github_actions_ci/tests-dx.sh