removes unused references from header of sorted BAM/CRAM files.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
*.bam{:bash}
Sorted BAM/CRAM file
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Removes unaligned references in aligned BAM alignment file
