Write consistent column sets to variant information files #1091
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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 |