samtools_flagstat

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

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install samtools/flagstat

https://github.com/CCBR/nf-modules/…/modules/CCBR/samtools/flagstat/

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
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
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
flagstat	file	File containing samtools flagstat output	*.{flagstat}
versions	file	File containing software versions	versions.yml

Tools

samtools

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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.