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ci.yml
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name: CI
on:
push:
branches:
- dev
- main
- ci
pull_request:
branches:
- dev
- main
- fix_vcf
release:
types: [published]
jobs:
preload_ancestry:
uses: ./.github/workflows/preload-reference.yml
preload_docker:
uses: ./.github/workflows/preload-docker.yml
preload_singularity:
uses: ./.github/workflows/preload-singularity.yml
standard_test_docker:
needs: preload_docker
uses: ./.github/workflows/standard-test.yml
with:
cache-key: ${{ needs.preload_docker.outputs.cache-key }}
docker: true
standard_test_singularity:
needs: preload_singularity
uses: ./.github/workflows/standard-test.yml
with:
cache-key: ${{ needs.preload_singularity.outputs.cache-key }}
singularity: true
pytest_workflow_docker:
needs: preload_docker
uses: ./.github/workflows/module.yml
strategy:
matrix:
tags:
- "test input check subworkflow"
- "test input check subworkflow with PGS catalog API"
- "test input check subworkflow with PGS catalog API and whitespace"
- "test make compatible subworkflow with bfile"
- "test make compatible subworkflow with vcf"
- "test make compatible subworkflow with pfile"
- "test input check subworkflow with liftover 38to37"
- "test input check subworkflow with liftover 37to38"
- "test apply score subworkflow"
- "test perfect apply score"
- "test combine scorefiles module"
- "test match module"
- "test match combine module"
- "plink2 testrelabelpvar"
- "plink2 testscore"
- "plink2 testsmallscore"
- "plink2 testmultiscore"
- "plink2 testsmallmultiscore"
- "plink2 testmultiscorefail"
- "plink2 vcf"
- "plink2 testrelabelbim"
- "pgscatalog test --pgs_id"
- "pgscatalog test --efo_trait --pgp_id and --pgs_id"
- "pgscatalog test bad accession"
- "pgscatalog test good and bad accessions GRCh38"
with:
cache-key: ${{ needs.preload_docker.outputs.cache-key }}
docker: true
tag: ${{ matrix.tags }}
pytest_workflow_singularity:
needs: preload_singularity
uses: ./.github/workflows/module.yml
strategy:
matrix:
tags:
- "test input check subworkflow"
- "test input check subworkflow with PGS catalog API"
- "test input check subworkflow with PGS catalog API and whitespace"
- "test make compatible subworkflow with bfile"
- "test make compatible subworkflow with vcf"
- "test make compatible subworkflow with pfile"
- "test input check subworkflow with liftover 38to37"
- "test input check subworkflow with liftover 37to38"
- "test apply score subworkflow"
- "test perfect apply score"
- "test combine scorefiles module"
- "test match module"
- "test match combine module"
- "plink2 testrelabelpvar"
- "plink2 testscore"
- "plink2 testsmallscore"
- "plink2 testmultiscore"
- "plink2 testsmallmultiscore"
- "plink2 testmultiscorefail"
- "plink2 vcf"
- "plink2 testrelabelbim"
- "pgscatalog test --pgs_id"
- "pgscatalog test --efo_trait --pgp_id and --pgs_id"
- "pgscatalog test bad accession"
- "pgscatalog test good and bad accessions GRCh38"
with:
cache-key: ${{ needs.preload_singularity.outputs.cache-key }}
singularity: true
tag: ${{ matrix.tags }}
ancestry_docker:
needs: [preload_ancestry, preload_docker]
uses: ./.github/workflows/ancestry.yml
with:
container-cache-key: ${{ needs.preload_docker.outputs.cache-key }}
ancestry-cache-key: ${{ needs.preload_ancestry.outputs.cache-key }}
docker: true
ancestry_singularity:
needs: [preload_ancestry, preload_singularity]
uses: ./.github/workflows/ancestry.yml
with:
container-cache-key: ${{ needs.preload_singularity.outputs.cache-key }}
ancestry-cache-key: ${{ needs.preload_ancestry.outputs.cache-key }}
singularity: true
ancestry_vcf_docker:
needs: [preload_ancestry, preload_docker]
uses: ./.github/workflows/ancestry-vcf.yml
with:
container-cache-key: ${{ needs.preload_docker.outputs.cache-key }}
ancestry-cache-key: ${{ needs.preload_ancestry.outputs.cache-key }}
docker: true