Sorts BAM/SAM files based on a variety of picard specific criteria
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam:file
BAM/CRAM/SAM file
*.{bam,sam}
sort_order:string
Picard sort order type
unsorted|queryname|coordinate|duplicate|unknown
bam
*.bam:file
Sorted BAM/CRAM/SAM file
*.{bam}
versions
versions.yml:file
File containing software versions
versions.yml
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
