Assigns all the reads in a file to a single new read-group
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Sequence reads file, can be SAM/BAM/CRAM format
*.{bam,cram,sam}
meta2{:bash}
fasta{:bash}
Reference genome file
*.{fasta,fa,fasta.gz,fa.gz}
fai{:bash}
Reference genome index file
*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}
bam{:bash}
*.bam{:bash}
Output BAM file
*.{bam}
bai{:bash}
*.bai{:bash}
An optional BAM index file
*.{bai}
cram{:bash}
*.cram{:bash}
Output CRAM file
*.{cram}
versions_picard{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
picard{:bash}
The tool name
picard AddOrReplaceReadGroups --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.
