removes unused references from header of sorted BAM/CRAM files.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM/CRAM file
*.{bam,cram}
*.bam
Sorted BAM/CRAM file
versions_bamaligncleaner
${task.process}
:string
The name of the process
bamaligncleaner
The name of the tool
bamAlignCleaner --version | sed 's/.*version //'
:eval
The expression to obtain the version of the tool
versions
Removes unaligned references in aligned BAM alignment file
