Documentation edits (August 2024) #1158
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name: CI | |
on: | |
push: | |
branches: | |
- dev | |
- main | |
- ci | |
pull_request: | |
branches: | |
- dev | |
- main | |
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 | |
ancestry_vcf_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 |