subworkflows/bam_cnv_wisecondorx
A subworkflow for calling CNVs using WisecondorX
cnvbambedcramplotsgenomics
Input
Name (Type)
Description
Pattern
An input channel containing BAM/CRAM files and their indices
Structure: [ val(meta), path(bam), path(bai) ]
A channel containing the index of the reference FASTA file
Structure: [ val(meta3), path(fai) ]
A channel containing WisecondorX reference created with WisecondorX newref
Structure: [ val(meta4), path(reference) ]
Output
Name (Type)
Description
Pattern
A channel containing the BED files with CNV aberrations
Structure: [ val(meta), path(bed) ]
A channel containing TXT files with chromosome statistics
Structure: [ val(meta), path(txt) ]
A channel containing lists of chromosome plots
Structure: [ val(meta), [ path(png), path(png), … ] ]
included modules and subworkflows
maintainer
