nf-core/subworkflows
Browse the 62 subworkflows that are currently available as part of nf-core.
A subworkflow for calling CNVs using WisecondorX
cnvbambedcramplotsgenomics
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
umicollapse, index BAM file and run samtools stats, flagstat and idxstats
umidedupindexbamsamcram
Calculate contamination of the X-chromosome with ANGSD
angsdbamcontaminationdocounts
Samtools markduplicate SAM/BAM/CRAM file
markdupbamsamcram
Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.
ngscheckmateqcbamsnp
Produces comprehensive statistics from BAM file
statisticscountshs_metricswgs_metricsbamsamcram
Subworkflow to run multiple commands in the RSeqC package
rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin
Split the reads in the input bam by specified genomic region.
splitbamsamcramindex