Convert and filter aligned reads to .npz
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
Reads in BAM/CRAM format
*.{bam,cram}
bai{:bash}
index of the BAM/CRAM file
*.{bai,crai}
meta2{:bash}
Groovy Map containing reference fasta meta information e.g. [ id:‘test’ ]
fasta{:bash}
The reference FASTA file (mandatory when using CRAM files)
*.{fasta,fa,fna}
meta3{:bash}
Groovy Map containing reference fasta index meta information e.g. [ id:‘test’ ]
fasta_fai{:bash}
The index of the reference FASTA file (mandatory when using CRAM files)
*.fai
npz{:bash}
*.npz{:bash}
The output NPZ file
*.npz
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
