Cleanup + update modules #5986
maxulysseci.yml
on: pull_request
Check for changes (nf-test)
4s
Check for changes (pytest)
3s
Matrix: nftest
Matrix: pytest
confirm-pass
0s
Annotations
40 warnings
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validation_checks docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/createsequencedictionary docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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gatk4/mergemutectstats docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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ngscheckmate docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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ngscheckmate docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/applyvqsr docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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gatk4/getpileupsummaries docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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gatk4/getpileupsummaries docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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skip_all_qc docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/calculatecontamination docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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skip_all_qc docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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validation_checks docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/calculatecontamination docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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tumor_normal_pair docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/filtermutectcalls docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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alignment_to_fastq docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/filtermutectcalls docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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gatk4/applyvqsr docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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gatk4/createsequencedictionary docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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save_output_as_bam_only docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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bwamem docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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default docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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alignment_to_fastq docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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umi docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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umi docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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bwamem docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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gatk4/mergemutectstats docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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save_mapped_only docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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default docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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save_output_as_bam_only docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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save_mapped_only docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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pipeline_sarek test,docker NF
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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tumor_normal_pair docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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joint_germline docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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skip_markduplicates docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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cnvkit docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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cnvkit docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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mutect2 docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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mutect2 docker NF 23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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skip_markduplicates docker NF latest-everything
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, 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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