Convert and filter aligned reads to .npz
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
Reads in BAM/CRAM format
*.{bam,cram}
bai
index of the BAM/CRAM file
*.{bai,crai}
meta2
Groovy Map containing reference fasta meta information e.g. [ id:‘test’ ]
fasta
The reference FASTA file (mandatory when using CRAM files)
*.{fasta,fa,fna}
meta3
Groovy Map containing reference fasta index meta information e.g. [ id:‘test’ ]
fasta_fai
The index of the reference FASTA file (mandatory when using CRAM files)
*.fai
npz
*.npz
The output NPZ file
versions_wisecondorx
${task.process}
:string
The name of the process
wisecondorx
The name of the tool
pip list |& sed -n 's/wisecondorx *//p'
:eval
The expression to obtain the version of the tool
versions
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
