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