shuffles and groups reads together by their names
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2
fasta
FASTA ref file
*.fasta
bam
*.bam
Sorted BAM
*.{bam}
cram
*.cram
Sorted CRAM
*.{cram}
sam
*.sam
Sorted SAM
*.{sam}
versions
versions.yml
File containing software versions
Tools for dealing with SAM, BAM and CRAM files
