bam_cnv_wisecondorx

A subworkflow for calling CNVs using WisecondorX

cnvbambedcramplotsgenomics

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_cnv_wisecondorx

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