Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
FASTA ref file
*.fasta
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
samtoolscalmd
MIT
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
