move env #1
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name: Run ancestry test with singularity or docker profiles | ||
on: | ||
workflow_call: | ||
inputs: | ||
container-cache-key: | ||
type: string | ||
required: true | ||
ancestry-cache-key: | ||
type: string | ||
required: true | ||
docker: | ||
type: boolean | ||
singularity: | ||
type: boolean | ||
env: | ||
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity | ||
SINGULARITY_VERSION: 3.8.3 | ||
jobs: | ||
docker: | ||
if: ${{ inputs.docker }} | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Set environment variables | ||
run: | | ||
echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v3 | ||
- uses: nf-core/setup-nextflow@v1 | ||
- name: Restore docker images | ||
id: restore-docker | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: ${{ runner.temp }}/docker | ||
key: ${{ inputs.container-cache-key }} | ||
fail-on-cache-miss: true | ||
- name: Load docker images from cache | ||
run: | | ||
find $HOME -name '*.tar' | ||
find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \; | ||
- name: Restore reference data | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: | | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst | ||
${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst | ||
key: ${{ inputs.ancestry-cache-key }} | ||
fail-on-cache-miss: true | ||
- name: Set up test requirements | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.10' | ||
cache: 'pip' | ||
- run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
- name: Run ancestry test | ||
run: TMPDIR=~ PROFILE=docker pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin | ||
- name: Upload logs on failure | ||
if: failure() | ||
uses: actions/upload-artifact@v3 | ||
with: | ||
name: logs-singularity-ancestry | ||
path: | | ||
/home/runner/pytest_workflow_*/*/.nextflow.log | ||
/home/runner/pytest_workflow_*/*/log.out | ||
/home/runner/pytest_workflow_*/*/log.err | ||
/home/runner/pytest_workflow_*/*/output/* | ||
singularity: | ||
if: ${{ inputs.singularity }} | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Set environment variables | ||
run: | | ||
echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v3 | ||
- uses: nf-core/setup-nextflow@v1 | ||
- name: Restore singularity setup | ||
id: restore-singularity-setup | ||
uses: actions/cache@v3 | ||
with: | ||
path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | ||
key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | ||
fail-on-cache-miss: true | ||
- name: Add singularity to path | ||
run: | | ||
echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH | ||
- name: Restore singularity container images | ||
id: restore-singularity | ||
uses: actions/cache@v3 | ||
with: | ||
path: ${{ env.NXF_SINGULARITY_CACHEDIR }} | ||
key: ${{ inputs.container-cache-key }} | ||
- name: Restore reference data | ||
uses: actions/cache/restore@v3 | ||
with: | ||
path: | | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam | ||
${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst | ||
${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst | ||
key: ${{ inputs.ancestry-cache-key }} | ||
fail-on-cache-miss: true | ||
- name: Set up test requirements | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.10' | ||
cache: 'pip' | ||
- run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
- name: Run ancestry test | ||
run: TMPDIR=~ PROFILE=singularity pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin | ||
env: | ||
TMPDIR: ${{ runner.temp }} | ||
- name: Upload logs on failure | ||
if: failure() | ||
uses: actions/upload-artifact@v3 | ||
with: | ||
name: logs-singularity-ancestry | ||
path: | | ||
/home/runner/pytest_workflow_*/*/.nextflow.log | ||
/home/runner/pytest_workflow_*/*/log.out | ||
/home/runner/pytest_workflow_*/*/log.err | ||
/home/runner/pytest_workflow_*/*/output/* |