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

pytest-changes

pre-commit

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

nf-test (bclconvert, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, nf-core/setup-nextflow@v1, 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/.

nf-test (bclconvert, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, nf-core/setup-nextflow@v1, actions/cache@v3, eWaterCycle/setup-apptainer@main, 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/.

nf-test (bcftools/view, docker)

nf-test (hamronization/amrfinderplus, docker)

nf-test (rsem/preparereference, docker)

nf-test (hamronization/abricate, docker)

nf-test (hamronization/summarize, docker)

nf-test (hamronization/amrfinderplus, singularity)

nf-test (rhocall/viz, docker)

nf-test (hamronization/abricate, singularity)

nf-test (hamronization/deeparg, docker)

nf-test (rhocall/viz, conda)

nf-test (bcftools/view, singularity)

nf-test (rhocall/viz, singularity)

nf-test (rsem/preparereference, conda)

nf-test (hamronization/fargene, docker)

nf-test (hamronization/summarize, singularity)

nf-test (subworkflows/bam_rseqc, docker)

nf-test (hamronization/amrfinderplus, conda)

nf-test (bcftools/view, conda)

nf-test (hamronization/deeparg, singularity)

nf-test (hamronization/abricate, conda)

nf-test (rsem/preparereference, singularity)

nf-test (rseqc/bamstat, docker)

nf-test (subworkflows/fastq_align_hisat2, docker)

nf-test (subworkflows/bam_rseqc, singularity)

nf-test (tximeta/tximport, singularity)

nf-test (subworkflows/preprocess_rnaseq, singularity)

nf-test (subworkflows/fastq_align_hisat2, singularity)

nf-core-lint (bclconvert)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/cache@v3, actions/setup-java@v3, nf-core/setup-nextflow@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (subworkflows/preprocess_rnaseq, docker)

nf-core-lint (antismash/antismashlitedownloaddatabases)

nf-test (custom/tx2gene, singularity)

nf-core-lint (custom/tx2gene)

nf-core-lint (deeparg/downloaddata)

nf-core-lint (bcftools/view)

nf-core-lint (rhocall/viz)

nf-core-lint (rseqc/bamstat)

nf-test (hamronization/rgi, docker)

nf-core-lint (rsem/preparereference)

nf-core-lint (sortmerna)

nf-core-lint (hamronization/rgi)

nf-core-lint (gsea/gsea)

nf-core-lint (hamronization/amrfinderplus)

nf-test (sortmerna, singularity)

nf-test (sortmerna, docker)

nf-test (hamronization/summarize, conda)

nf-core-lint (hamronization/abricate)

nf-core-lint (deeparg/predict)

nf-test (wfmash, conda)

nf-core-lint (hamronization/deeparg)

nf-test (rseqc/bamstat, singularity)

nf-core-lint (subworkflows/bam_rseqc)

nf-core-lint (hamronization/summarize)

nf-test (hamronization/deeparg, conda)

nf-core-lint (hamronization/fargene)

nf-core-lint (subworkflows/fastq_align_hisat2)

nf-core-lint (tximeta/tximport)

nf-test (hamronization/fargene, conda)

nf-core-lint (subworkflows/preprocess_rnaseq)

nf-test (wfmash, docker)

nf-test (wfmash, singularity)

nf-core-lint (wfmash)

nf-test (tximeta/tximport, docker)

nf-test (hamronization/fargene, singularity)

nf-test (subworkflows/preprocess_rnaseq, conda)

nf-test (subworkflows/bam_rseqc, conda)

nf-test (hamronization/rgi, conda)

nf-test (rseqc/bamstat, conda)

nf-test (tximeta/tximport, conda)

nf-test (subworkflows/fastq_align_hisat2, conda)

nf-test (custom/tx2gene, docker)

pytest (gsea/gsea, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/github-script@v6. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (gsea/gsea, conda)

nf-test (hamronization/rgi, singularity)

pytest (gsea/gsea, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/github-script@v6. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (deeparg/predict, singularity)