Sorts BAM/SAM files based on a variety of picard specific criteria
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM/SAM file
*.{bam,sam}
sort_order{:bash}
:string
Picard sort order type
unsorted|queryname|coordinate|duplicate|unknown
*.bam{:bash}
Sorted BAM/CRAM/SAM file
*.{bam}
versions_picard{:bash}
${task.process}{:bash}
The process the versions were collected from
picard{:bash}
The tool name
picard SortSam --version 2>&1 | sed -n 's/.*Version://p'{:bash}
The command used to generate the version of the tool
versions{:bash}
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
