Use groovy to parse samplesheets #856
nebfieldci.yml
on: pull_request
preload_docker
/
docker
2m 58s
preload_singularity
/
singularity
1m 28s
preload_ancestry
/
preload_reference
14s
Matrix: pytest_workflow_docker
Matrix: standard_test_docker / docker
Matrix: standard_test_docker / singularity
Matrix: pytest_workflow_singularity
Matrix: standard_test_singularity / docker
Matrix: standard_test_singularity / singularity
ancestry_docker
/
docker
4m 4s
ancestry_docker
/
singularity
0s
ancestry_vcf_docker
/
docker
4m 44s
ancestry_vcf_docker
/
singularity
0s
ancestry_singularity
/
docker
0s
ancestry_singularity
/
singularity
3m 55s
ancestry_vcf_singularity
/
docker
0s
ancestry_vcf_singularity
/
singularity
4m 1s
Annotations
61 warnings
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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/.
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preload_singularity / singularity
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/.
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pytest_workflow_singularity (plink2 testrelabelbim) / 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/.
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pytest_workflow_singularity (plink2 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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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pytest_workflow_singularity (plink2 testmultiscore) / 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/.
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pytest_workflow_singularity (pgscatalog test bad accession) / 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/.
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pytest_workflow_singularity (pgscatalog test --pgs_id) / 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/.
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pytest_workflow_singularity (test make compatible subworkflow with pfile) / 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/.
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pytest_workflow_singularity (plink2 testsmallscore) / 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/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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pytest_workflow_singularity (plink2 testsmallmultiscore) / 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/.
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pytest_workflow_singularity (test match module) / 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/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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standard_test_singularity / singularity (test, singularity, 22.10.0)
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/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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pytest_workflow_singularity (test input check subworkflow with liftover 38to37) / 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/.
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pytest_workflow_singularity (test match combine module) / 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/.
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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/.
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pytest_workflow_singularity (plink2 testrelabelpvar) / 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/.
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pytest_workflow_singularity (plink2 testscore) / 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/.
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pytest_workflow_singularity (test perfect apply score) / 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/.
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pytest_workflow_singularity (pgscatalog test good and bad accessions GRCh38) / 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/.
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pytest_workflow_singularity (test make compatible subworkflow with bfile) / 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/.
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pytest_workflow_singularity (test apply score 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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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preload_docker / docker
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/.
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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/.
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pytest_workflow_singularity (pgscatalog test --efo_trait --pgp_id and --pgs_id) / 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/.
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pytest_workflow_docker (pgscatalog test bad accession) / 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/.
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pytest_workflow_docker (pgscatalog test good and bad accessions GRCh38) / 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/.
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pytest_workflow_docker (test input check subworkflow) / 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/.
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pytest_workflow_docker (plink2 testmultiscore) / 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/.
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pytest_workflow_docker (plink2 testrelabelbim) / 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/.
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pytest_workflow_docker (test match module) / 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/.
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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/.
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pytest_workflow_docker (plink2 testsmallscore) / 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/.
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pytest_workflow_docker (test input check subworkflow with PGS catalog API) / 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/.
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pytest_workflow_docker (plink2 testsmallmultiscore) / 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/.
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pytest_workflow_docker (plink2 testscore) / 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/.
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pytest_workflow_docker (test match combine module) / 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/.
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pytest_workflow_docker (pgscatalog test --pgs_id) / 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/.
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pytest_workflow_docker (test apply score subworkflow) / 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/.
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pytest_workflow_docker (plink2 testmultiscorefail) / 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/.
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pytest_workflow_docker (test perfect apply score) / 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/.
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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/.
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standard_test_docker / docker (test, docker, 22.10.0)
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/.
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pytest_workflow_docker (test input check subworkflow with liftover 38to37) / 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/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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pytest_workflow_docker (test make compatible subworkflow with 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/.
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pytest_workflow_docker (test input check subworkflow with liftover 37to38) / 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/.
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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. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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pytest_workflow_docker (plink2 testrelabelpvar) / 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/.
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pytest_workflow_docker (test input check subworkflow with PGS catalog API and whitespace) / 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/.
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pytest_workflow_singularity (test combine scorefiles module) / 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/.
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ancestry_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/.
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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/.
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pytest_workflow_docker (pgscatalog test --efo_trait --pgp_id and --pgs_id) / 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/.
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ancestry_docker / 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/.
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ancestry_vcf_docker / 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/.
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pytest_workflow_docker (test combine scorefiles module) / 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/.
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