Use groovy to parse samplesheets #855

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (plink2 testmultiscorefail) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (plink2 testrelabelpvar) / singularity

pytest_workflow_singularity (plink2 testmultiscore) / singularity

pytest_workflow_singularity (test match combine module) / singularity

pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / singularity

preload_docker / docker

pytest_workflow_singularity (test input check subworkflow) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test input check subworkflow) / singularity

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

standard_test_singularity / singularity (test, singularity, latest)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@v1, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test input check subworkflow with PGS catalog API) / singularity

pytest_workflow_singularity (test perfect apply score) / singularity

pytest_workflow_singularity (plink2 testrelabelbim) / singularity

standard_test_singularity / singularity (test, singularity, 22.10.0)

pytest_workflow_singularity (pgscatalog test --pgs_id) / singularity

pytest_workflow_singularity (pgscatalog test bad accession) / singularity

pytest_workflow_singularity (plink2 vcf) / singularity

pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test input check subworkflow with liftover 37to38) / singularity

pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test input check subworkflow with PGS catalog API and whitespace) / singularity

pytest_workflow_singularity (test match module) / singularity

pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_singularity (test make compatible subworkflow with vcf) / singularity

pytest_workflow_singularity (test make compatible subworkflow with pfile) / singularity

pytest_workflow_singularity (plink2 testsmallmultiscore) / singularity

pytest_workflow_singularity (plink2 testscore) / singularity

pytest_workflow_singularity (plink2 testsmallscore) / singularity

pytest_workflow_singularity (test apply score subworkflow) / singularity

pytest_workflow_singularity (test make compatible subworkflow with bfile) / singularity

pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / singularity

pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / singularity

pytest_workflow_singularity (test combine scorefiles module) / singularity

pytest_workflow_docker (plink2 vcf) / docker

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache/restore@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_docker (pgscatalog test bad accession) / docker

pytest_workflow_docker (plink2 testmultiscorefail) / docker

pytest_workflow_docker (test match module) / docker

pytest_workflow_docker (plink2 testrelabelbim) / docker

pytest_workflow_docker (test match combine module) / docker

standard_test_docker / docker (test, docker, latest)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@v1, actions/cache/restore@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_docker (plink2 testsmallmultiscore) / docker

pytest_workflow_docker (pgscatalog test --pgs_id) / docker

pytest_workflow_docker (plink2 testsmallscore) / docker

pytest_workflow_docker (plink2 testmultiscore) / docker

pytest_workflow_docker (test make compatible subworkflow with pfile) / docker

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache/restore@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_docker (test make compatible subworkflow with pfile) / docker

pytest_workflow_docker (plink2 testrelabelpvar) / docker

pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / docker

pytest_workflow_docker (test perfect apply score) / docker

pytest_workflow_docker (test make compatible subworkflow with bfile) / docker

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache/restore@v3, actions/setup-python@v3, actions/upload-artifact@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest_workflow_docker (test make compatible subworkflow with bfile) / docker

standard_test_docker / docker (test, docker, 22.10.0)

pytest_workflow_docker (test make compatible subworkflow with vcf) / docker

pytest_workflow_docker (test input check subworkflow with PGS catalog API) / docker

pytest_workflow_docker (test apply score subworkflow) / docker

pytest_workflow_docker (plink2 testscore) / docker

pytest_workflow_docker (test input check subworkflow with liftover 38to37) / docker

pytest_workflow_docker (test input check subworkflow) / docker

pytest_workflow_docker (test input check subworkflow with liftover 37to38) / docker

pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / docker

pytest_workflow_docker (test combine scorefiles module) / docker

pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / docker

preload_ancestry / preload_reference

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

ancestry_vcf_singularity / singularity

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, nf-core/setup-nextflow@v1, actions/cache@v3, actions/cache/restore@v3, actions/setup-python@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

ancestry_singularity / singularity

ancestry_docker / docker

ancestry_vcf_docker / docker

Artifacts

Produced during runtime

Name	Size
logs-docker-test make compatible subworkflow with pfile Expired	1.14 MB
logs-singularity-test input check subworkflow Expired	106 KB
logs-singularity-test input check subworkflow with PGS catalog API Expired	2.75 MB
logs-singularity-test input check subworkflow with liftover 37to38 Expired	5.82 MB

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Use groovy to parse samplesheets #855

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Use groovy to parse samplesheets #855

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