Modify subworkflows to pass new nf-core linting #18134

Run time

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Job	Run time
Check for changes	4s
subworkflows/bam_create_som_pon_gatk docker	15m 52s
subworkflows/bam_create_som_pon_gatk singularity	16m 16s
subworkflows/bam_create_som_pon_gatk conda	15m 38s
subworkflows/bam_dedup_stats_samtools_umitools docker	1m 5s
subworkflows/bam_dedup_stats_samtools_umitools singularity	4m 11s
subworkflows/bam_dedup_stats_samtools_umitools conda	2m 57s
subworkflows/bam_docounts_contamination_angsd docker	1m 11s
subworkflows/bam_docounts_contamination_angsd singularity	3m 16s
subworkflows/bam_docounts_contamination_angsd conda	3m 12s
subworkflows/bam_markduplicates_picard docker	1m 43s
subworkflows/bam_markduplicates_picard singularity	5m 43s
subworkflows/bam_markduplicates_picard conda	4m 0s
subworkflows/bam_markduplicates_samtools docker	59s
subworkflows/bam_markduplicates_samtools singularity	3m 55s
subworkflows/bam_markduplicates_samtools conda	2m 17s
subworkflows/bam_ngscheckmate docker	1m 30s
subworkflows/bam_ngscheckmate singularity	3m 57s
subworkflows/bam_ngscheckmate conda	5m 27s
subworkflows/bam_qc_picard docker	2m 2s
subworkflows/bam_qc_picard singularity	5m 5s
subworkflows/bam_qc_picard conda	4m 56s
subworkflows/bam_rseqc docker	1m 16s
subworkflows/bam_rseqc singularity	4m 47s
subworkflows/bam_rseqc conda	3m 34s
subworkflows/bam_sort_stats_samtools docker	7m 48s
subworkflows/bam_sort_stats_samtools singularity	11m 15s
subworkflows/bam_sort_stats_samtools conda	18m 53s
subworkflows/bam_split_by_region docker	1m 6s
subworkflows/bam_split_by_region singularity	3m 50s
subworkflows/bam_split_by_region conda	3m 6s
subworkflows/bam_stats_samtools docker	8m 53s
subworkflows/bam_stats_samtools singularity	14m 52s
subworkflows/bam_stats_samtools conda	23m 17s
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk docker	7m 16s
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk singularity	10m 56s
subworkflows/bam_tumor_normal_somatic_variant_calling_gatk conda	9m 18s
subworkflows/bam_tumor_only_somatic_variant_calling_gatk docker	7m 13s
subworkflows/bam_tumor_only_somatic_variant_calling_gatk singularity	13m 19s
subworkflows/bam_tumor_only_somatic_variant_calling_gatk conda	11m 11s
subworkflows/bam_variant_calling_sort_freebayes_bcftools docker	1m 20s
subworkflows/bam_variant_calling_sort_freebayes_bcftools singularity	3m 21s
subworkflows/bam_variant_calling_sort_freebayes_bcftools conda	3m 17s
subworkflows/bam_variant_demix_boot_freyja docker	6m 39s
subworkflows/bam_variant_demix_boot_freyja singularity	8m 2s
subworkflows/bam_variant_demix_boot_freyja conda	7m 36s
subworkflows/bcl_demultiplex docker	1m 3s
subworkflows/bcl_demultiplex singularity	5m 10s
subworkflows/bed_scatter_bedtools docker	51s
subworkflows/bed_scatter_bedtools singularity	3m 11s
subworkflows/bed_scatter_bedtools conda	2m 12s
subworkflows/bedgraph_bedclip_bedgraphtobigwig docker	51s
subworkflows/bedgraph_bedclip_bedgraphtobigwig singularity	3m 35s
subworkflows/bedgraph_bedclip_bedgraphtobigwig conda	3m 8s
subworkflows/fasta_binning_concoct docker	1m 36s
subworkflows/fasta_binning_concoct singularity	7m 20s
subworkflows/fasta_binning_concoct conda	3m 21s
subworkflows/fasta_clean_fcs docker	4m 10s
subworkflows/fasta_clean_fcs singularity	7m 44s
subworkflows/fasta_index_dna docker	1m 49s
subworkflows/fasta_index_dna singularity	4m 36s
subworkflows/fasta_index_dna conda	5m 54s
subworkflows/fasta_newick_epang_gappa docker	2m 57s
subworkflows/fasta_newick_epang_gappa singularity	5m 56s
subworkflows/fasta_newick_epang_gappa conda	6m 0s
subworkflows/fastq_align_bowtie2 docker	1m 14s
subworkflows/fastq_align_bowtie2 singularity	3m 45s
subworkflows/fastq_align_bowtie2 conda	4m 39s
subworkflows/fastq_align_bwa docker	1m 4s
subworkflows/fastq_align_bwa singularity	3m 45s
subworkflows/fastq_align_bwa conda	4m 17s
subworkflows/fastq_align_bwaaln docker	1m 58s
subworkflows/fastq_align_bwaaln singularity	3m 58s
subworkflows/fastq_align_bwaaln conda	6m 29s
subworkflows/fastq_align_chromap docker	1m 26s
subworkflows/fastq_align_chromap singularity	4m 31s
subworkflows/fastq_align_chromap conda	4m 10s
subworkflows/fastq_align_dna docker	3m 23s
subworkflows/fastq_align_dna singularity	6m 48s
subworkflows/fastq_align_dna conda	10m 34s
subworkflows/fastq_align_hisat2 docker	1m 19s
subworkflows/fastq_align_hisat2 singularity	4m 19s
subworkflows/fastq_align_hisat2 conda	4m 45s
subworkflows/fastq_align_star docker	4m 22s
subworkflows/fastq_align_star singularity	7m 13s
subworkflows/fastq_align_star conda	7m 38s
subworkflows/fastq_contam_seqtk_kraken docker	1m 0s
subworkflows/fastq_contam_seqtk_kraken singularity	3m 33s
subworkflows/fastq_contam_seqtk_kraken conda	4m 3s
subworkflows/fastq_create_umi_consensus_fgbio docker	4m 10s
subworkflows/fastq_create_umi_consensus_fgbio singularity	7m 29s
subworkflows/fastq_create_umi_consensus_fgbio conda	7m 19s
subworkflows/fastq_download_prefetch_fasterqdump_sratools docker	1m 39s
subworkflows/fastq_download_prefetch_fasterqdump_sratools singularity	5m 32s
subworkflows/fastq_download_prefetch_fasterqdump_sratools conda	4m 13s
subworkflows/fastq_fastqc_umitools_fastp docker	1m 0s
subworkflows/fastq_fastqc_umitools_fastp singularity	3m 54s
subworkflows/fastq_fastqc_umitools_fastp conda	3m 45s
subworkflows/fastq_fastqc_umitools_trimgalore docker	2m 53s
subworkflows/fastq_fastqc_umitools_trimgalore singularity	5m 44s
subworkflows/fastq_fastqc_umitools_trimgalore conda	6m 11s
subworkflows/fastq_subsample_fq_salmon docker	1m 34s
subworkflows/fastq_subsample_fq_salmon singularity	3m 45s
subworkflows/fastq_subsample_fq_salmon conda	3m 2s
subworkflows/fastq_trim_fastp_fastqc docker	3m 30s
subworkflows/fastq_trim_fastp_fastqc singularity	7m 35s
subworkflows/fastq_trim_fastp_fastqc conda	4m 9s
subworkflows/homer/groseq docker	33s
subworkflows/homer/groseq singularity	3m 25s
subworkflows/homer/groseq conda	1m 32s
subworkflows/multiple_impute_glimpse2 docker	2m 12s
subworkflows/multiple_impute_glimpse2 singularity	4m 53s
subworkflows/multiple_impute_glimpse2 conda	6m 10s
subworkflows/vcf_annotate_ensemblvep docker	3m 31s
subworkflows/vcf_annotate_ensemblvep singularity	7m 9s
subworkflows/vcf_annotate_ensemblvep conda	7m 48s
subworkflows/vcf_annotate_ensemblvep_snpeff docker	10m 42s
subworkflows/vcf_annotate_ensemblvep_snpeff singularity	21m 18s
subworkflows/vcf_annotate_ensemblvep_snpeff conda	9m 58s
subworkflows/vcf_annotate_snpeff docker	1m 17s
subworkflows/vcf_annotate_snpeff singularity	3m 37s
subworkflows/vcf_annotate_snpeff conda	3m 28s
subworkflows/vcf_extract_relate_somalier docker	2m 25s
subworkflows/vcf_extract_relate_somalier singularity	4m 53s
subworkflows/vcf_extract_relate_somalier conda	5m 44s
subworkflows/vcf_gather_bcftools docker	1m 13s
subworkflows/vcf_gather_bcftools singularity	4m 1s
subworkflows/vcf_gather_bcftools conda	3m 32s
subworkflows/vcf_impute_glimpse docker	1m 9s
subworkflows/vcf_impute_glimpse singularity	5m 3s
subworkflows/vcf_impute_glimpse conda	4m 0s
subworkflows/vcf_phase_shapeit5 docker	2m 37s
subworkflows/vcf_phase_shapeit5 singularity	6m 19s
subworkflows/vcf_phase_shapeit5 conda	5m 5s
	11h 19m 56s

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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 #18134

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