Assigns all the reads in a file to a single new read-group
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
meta2
meta3
reads
Sequence reads file, can be SAM/BAM/CRAM format
*.{bam,cram,sam}
fasta
Reference genome file
*.{fasta,fa,fasta.gz,fa.gz}
fasta_index
Reference genome index file
*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}
versions
File containing software versions
versions.yml
bam
Output BAM file
*.{bam}
bai
An optional BAM index file
*.{bai}
cram
Output CRAM file
*.{cram}
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
