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name: Run ancestry test with singularity or docker profiles | ||
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on: | ||
workflow_call: | ||
inputs: | ||
container-cache-key: | ||
type: string | ||
required: true | ||
ancestry-cache-key: | ||
type: string | ||
required: true | ||
docker: | ||
type: boolean | ||
singularity: | ||
type: boolean | ||
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env: | ||
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity | ||
SINGULARITY_VERSION: 3.8.3 | ||
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jobs: | ||
docker: | ||
if: ${{ inputs.docker }} | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- name: Set environment variables | ||
run: | | ||
echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v3 | ||
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- uses: nf-core/setup-nextflow@v1 | ||
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- 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 | ||
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- 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 | ||
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- name: Install plink2 to recode | ||
run: sudo apt-get install -y plink2 | ||
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- name: Make VCF | ||
run: | | ||
plink2 --pfile ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL vzs \ | ||
--export vcf bgz \ | ||
--out ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL | ||
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- name: Set up test requirements | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.10' | ||
cache: 'pip' | ||
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- run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
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- name: Run ancestry test | ||
run: TMPDIR=~ PROFILE=docker pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry vcf" --ignore tests/bin | ||
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- 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: ${{ inputs.singularity }} | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- name: Set environment variables | ||
run: | | ||
echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v3 | ||
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- uses: nf-core/setup-nextflow@v1 | ||
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- name: Restore singularity setup | ||
id: restore-singularity-setup | ||
uses: actions/cache@v3 | ||
with: | ||
path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64 | ||
key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }} | ||
fail-on-cache-miss: true | ||
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- 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 }} | ||
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- 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 | ||
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- name: Set up test requirements | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.10' | ||
cache: 'pip' | ||
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- run: pip install -r ${{ github.workspace }}/tests/requirements.txt | ||
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- name: Run ancestry test | ||
run: TMPDIR=~ PROFILE=singularity pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin | ||
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- 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/* |
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sampleset,path_prefix,chrom,format | ||
test,ANCESTRY_TARGET_DIR/GRCh38_HAPNEST_TARGET_ALL,,vcf |
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# ancestry test notes: | ||
# need to stage reference in $ANCESTRY_REF_DIR | ||
# extract target in $ANCESTRY_TARGET_DIR | ||
# need to convert target to VCF | ||
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- name: test ancestry projection and scoring | ||
command: > | ||
bash -c " | ||
sed \"s|ANCESTRY_TARGET_DIR|$ANCESTRY_TARGET_DIR|\" tests/ancestry/samplesheet.csv > samplesheet.csv; | ||
nextflow run main.nf -c ./tests/config/nextflow.config \ | ||
--input samplesheet.csv \ | ||
--run_ancestry $ANCESTRY_REF_DIR/GRCh38_HAPNEST_reference.tar.zst \ | ||
--target_build GRCh38 \ | ||
--pgs_id PGS001229 \ | ||
--min_overlap 0.50 \ | ||
--target_build GRCh38 \ | ||
--scorefile false | ||
" | ||
tags: | ||
- ancestry vcf | ||
- slow | ||
stdout: | ||
contains: | ||
- "Pipeline completed successfully" | ||
files: | ||
- path: "output/test/score/pop_summary.csv" | ||
contains: | ||
- "AFR,100 (33.33%)" | ||
- "EAS,100 (33.33%)" | ||
- "EUR,100 (33.33%)" |