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:map
fasta:file
Reference genome file
*.{fasta,fa,fasta.gz,fa.gz}
meta3:map
fasta_index:file
Reference genome index file
*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}
bam
*.bam:file
Output BAM file
*.{bam}
bai
*.bai:file
An optional BAM index file
*.{bai}
cram
*.cram:file
Output CRAM file
*.{cram}
versions
versions.yml:file
File containing software versions
versions.yml
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
