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{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
