nf-core/subworkflows

Browse the 43 subworkflows that are currently available as part of nf-core.

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bam_create_som_pon_gatk

Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.

gatk4mutect2genomicsdbimportcreatesomaticpanelofnormalsvariant_callinggenomicsdb_workspacepanel_of_normals

Includes: gatk4/mutect2 gatk4/genomicsdbimport gatk4/createsomaticpanelofnormals

bam_dedup_stats_samtools_umitools

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

Included in: nascent rnaseq

Includes: umitools/dedup samtools/index samtools/stats samtools/idxstats samtools/flagstat

bam_docounts_contamination_angsd

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts

Includes: angsd/docounts angsd/contamination

bam_markduplicates_picard

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

markduplicatesbamsamcram

Included in: atacseq circdna rnaseq +1 more pipelines

Includes: picard/markduplicates samtools/index samtools/stats samtools/idxstats samtools/flagstat

bam_ngscheckmate

Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

ngscheckmateqcbamsnp

Includes: bcftools/mpileup ngscheckmate/ncm

bam_qc_picard

Produces comprehensive statistics from BAM file

statisticscountshs_metricswgs_metricsbamsamcram

Includes: picard/collectmultiplemetrics picard/collectwgsmetrics picard/collecthsmetrics

bam_rseqc

Subworkflow to run multiple commands in the RSeqC package

rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin

Included in: callingcards rnaseq

Includes: rseqc

bam_sort_stats_samtools

Sort SAM/BAM/CRAM file

sortbamsamcram

Included in: atacseq circrna cutandrun +4 more pipelines

Includes: samtools/sort samtools/index samtools/stats samtools/idxstats samtools/flagstat

bam_split_by_region

Split the reads in the input bam by specified genomic region.

splitbamsamcramindex

Includes: samtools/view samtools/index

bam_stats_samtools

Produces comprehensive statistics from SAM/BAM/CRAM file

statisticscountsbamsamcram

Included in: atacseq callingcards circdna +6 more pipelines

Includes: samtools/stats samtools/idxstats samtools/flagstat

bam_tumor_normal_somatic_variant_calling_gatk

Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode. f1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors. Run the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.

gatk4mutect2learnreadorientationmodelgetpileupsummariescalculatecontaminationfiltermutectcallsvariant_callingtumor_onlyfiltered_vcf

Includes: gatk4/mutect2 gatk4/learnreadorientationmodel gatk4/getpileupsummaries gatk4/calculatecontamination gatk4/filtermutectcalls

bam_tumor_only_somatic_variant_calling_gatk

Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.

gatk4mutect2getpileupsummariescalculatecontaminationfiltermutectcallsvariant_callingtumor_onlyfiltered_vcf

Includes: gatk4/mutect2 gatk4/getpileupsummaries gatk4/calculatecontamination gatk4/filtermutectcalls