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Modify subworkflows to pass new nf-core linting #18134

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Modify subworkflows to pass new nf-core linting

Modify subworkflows to pass new nf-core linting #18134

Triggered via pull request July 27, 2023 07:19
@mirpedrolmirpedrol
synchronize #3672
mirpedrol:subworkflows-lint
Status Failure
Total duration 28m 44s
Artifacts 1

pytest-workflow.yml

on: pull_request
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Matrix: test
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6 errors and 133 warnings
subworkflows/fasta_binning_concoct conda
Process completed with exit code 1.
subworkflows/bam_qc_picard conda
Process completed with exit code 1.
subworkflows/fastq_align_bowtie2 conda
Process completed with exit code 1.
subworkflows/fastq_subsample_fq_salmon conda
Process completed with exit code 1.
subworkflows/fastq_trim_fastp_fastqc conda
Process completed with exit code 1.
subworkflows/vcf_annotate_ensemblvep_snpeff conda
Process completed with exit code 1.
subworkflows/bed_scatter_bedtools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bedgraph_bedclip_bedgraphtobigwig docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_samtools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_dedup_stats_samtools_umitools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bcl_demultiplex docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_split_by_region docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_docounts_contamination_angsd docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_rseqc docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_calling_sort_freebayes_bcftools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_ngscheckmate docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_binning_concoct docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_picard docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_qc_picard docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bed_scatter_bedtools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_samtools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bowtie2 docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwa docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_index_dna docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_dedup_stats_samtools_umitools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_split_by_region conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_docounts_contamination_angsd conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bedgraph_bedclip_bedgraphtobigwig conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_docounts_contamination_angsd singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bed_scatter_bedtools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_calling_sort_freebayes_bcftools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_calling_sort_freebayes_bcftools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_binning_concoct conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/bam_rseqc conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bedgraph_bedclip_bedgraphtobigwig singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_split_by_region singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_samtools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_ngscheckmate singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_picard conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_chromap docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_newick_epang_gappa docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwaaln docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_dedup_stats_samtools_umitools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_clean_fcs docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_contam_seqtk_kraken docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_hisat2 docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_rseqc singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_qc_picard conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/bam_qc_picard singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bowtie2 singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bcl_demultiplex singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_fastp docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_ngscheckmate conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwa singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_index_dna singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_markduplicates_picard singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwa conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_download_prefetch_fasterqdump_sratools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bowtie2 conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/fasta_index_dna conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/homer/groseq docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwaaln singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_dna docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_chromap conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_demix_boot_freyja docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_subsample_fq_salmon docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_newick_epang_gappa conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/homer/groseq conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_newick_epang_gappa singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_only_somatic_variant_calling_gatk docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_chromap singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_contam_seqtk_kraken singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_binning_concoct singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_trimgalore docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_demix_boot_freyja conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_hisat2 singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_contam_seqtk_kraken conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_star docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_sort_stats_samtools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fasta_clean_fcs singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_fastp conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_hisat2 conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_subsample_fq_salmon conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/multiple_impute_glimpse2 docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_create_umi_consensus_fgbio docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_variant_demix_boot_freyja singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_bwaaln conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_download_prefetch_fasterqdump_sratools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_fastp singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_snpeff docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_gather_bcftools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_trim_fastp_fastqc docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_stats_samtools docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_impute_glimpse docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_subsample_fq_salmon singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/homer/groseq singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_trim_fastp_fastqc conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/fastq_download_prefetch_fasterqdump_sratools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_extract_relate_somalier docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_ensemblvep docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_dna singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_snpeff conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_phase_shapeit5 docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_trimgalore singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_star singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/multiple_impute_glimpse2 singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_fastqc_umitools_trimgalore conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_gather_bcftools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_snpeff singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_star conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_only_somatic_variant_calling_gatk conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_create_umi_consensus_fgbio conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_sort_stats_samtools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_create_umi_consensus_fgbio singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_gather_bcftools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_impute_glimpse conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/multiple_impute_glimpse2 conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_extract_relate_somalier singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_phase_shapeit5 conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_impute_glimpse singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_extract_relate_somalier conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_trim_fastp_fastqc singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_tumor_only_somatic_variant_calling_gatk singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/fastq_align_dna conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_ensemblvep singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_ensemblvep conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_phase_shapeit5 singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_stats_samtools singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_create_som_pon_gatk conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_create_som_pon_gatk docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_create_som_pon_gatk singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_ensemblvep_snpeff conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, 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/
subworkflows/vcf_annotate_ensemblvep_snpeff docker
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_sort_stats_samtools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/bam_stats_samtools conda
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
subworkflows/vcf_annotate_ensemblvep_snpeff singularity
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2, eWaterCycle/setup-singularity@v5. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Artifacts

Produced during runtime
Name Size
logs-conda- Expired
306 MB