Find copy number aberrations
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
npz{:bash}
:file
An NPZ file created with WisecondorX convert
*.npz
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
reference{:bash}
A reference NPZ file created with WisecondorX newref
meta3{:bash}
blacklist{:bash}
OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)
*.bed
aberrations_bed{:bash}
*_aberrations.bed
*_aberrations.bed{:bash}
bins_bed{:bash}
*_bins.bed{:bash}
*_bins.bed
segments_bed{:bash}
*_segments.bed{:bash}
*_segments.bed
chr_statistics{:bash}
*_statistics.txt{:bash}
*_chr_statistics.txt
chr_plots{:bash}
[!genome_wide]*.png{:bash}
[!genome_wide]*.png
genome_plot{:bash}
genome_wide.png{:bash}
genome_wide.png
versions_wisecondorx{:bash}
${task.process}{:bash}
:string
The name of the process
wisecondorx{:bash}
The name of the tool
pip list |& sed -n 's/wisecondorx *//p'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
