Description

Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

bam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai:file

Index for BAM/CRAM/SAM file

*.{bai,crai,sai}

Output

name:type
description
pattern

flagstat

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.flagstat:file

File containing samtools flagstat output

*.{flagstat}

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.