Assigns all the reads in a file to a single new read-group
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
Sequence reads file, can be SAM/BAM/CRAM format
*.{bam,cram,sam}
meta2
fasta
Reference genome file
*.{fasta,fa,fasta.gz,fa.gz}
fai
Reference genome index file
*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}
bam
*.bam
Output BAM file
*.{bam}
bai
*.bai
An optional BAM index file
*.{bai}
cram
*.cram
Output CRAM file
*.{cram}
versions_picard
${task.process}
:string
The process the versions were collected from
picard
The tool name
picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'
The command used to generate the version of the tool
versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
