Groovy Map containing sample information
e.g. [ id:‘test’ ]
input:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
intervals:file
Interval FILE
*.bed
meta2:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
fasta:file
FASTA reference file
*.{fasta,fa}
Output
name:type
description
pattern
mpileup
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.mpileup.gz:file
mpileup file
*.{mpileup}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
samtools
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.
