Description

A subworkflow for calling CNVs using WisecondorX

Input

name:type
description
pattern

ch_bam

An input channel containing BAM/CRAM files and their indices
Structure: [ val(meta), path(bam), path(bai) ]

ch_fasta

A channel containing the reference FASTA file
Structure: [ val(meta2), path(fasta) ]

ch_fai

A channel containing the index of the reference FASTA file
Structure: [ val(meta3), path(fai) ]

ch_ref

A channel containing WisecondorX reference created with WisecondorX newref
Structure: [ val(meta4), path(reference) ]

ch_blacklist

An optional channel containing a BED file with regions to mask from the analyis
Structure: [ val(meta5), path(blacklist) ]

Output

name:type
description
pattern

aberrations_bed

A channel containing the BED files with CNV aberrations
Structure: [ val(meta), path(bed) ]

bins_bed

A channel containing the BED files with the used bins
Structure: [ val(meta), path(bed) ]

segments_bed

A channel containing the segment BED files
Structure: [ val(meta), path(bed) ]

chr_statistics

A channel containing TXT files with chromosome statistics
Structure: [ val(meta), path(txt) ]

chr_plots

A channel containing lists of chromosome plots
Structure: [ val(meta), [ path(png), path(png), … ] ]

genome_plot

A channel containing the plots of the whole genomes
Structure: [ val(meta), path(png) ]

versions :file

File containing software versions

versions.yml