Convert and filter aligned reads to .npz
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
Reads in BAM/CRAM format
*.{bam,cram}
bai:file
index of the BAM/CRAM file
*.{bai,crai}
meta2:map
Groovy Map containing reference fasta meta information e.g. [ id:‘test’ ]
fasta:file
The reference FASTA file (mandatory when using CRAM files)
*.{fasta,fa,fna}
meta3:map
Groovy Map containing reference fasta index meta information e.g. [ id:‘test’ ]
fasta_fai:file
The index of the reference FASTA file (mandatory when using CRAM files)
*.fai
npz
*.npz:file
The output NPZ file
*.npz
versions
versions.yml:file
File containing software versions
versions.yml
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
