name: samtools_flagstat description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type keywords: - stats - mapping - counts - bam - sam - cram tools: - samtools: description: | 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. homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - bai: type: file description: Index for BAM/CRAM/SAM file pattern: "*.{bai,crai,sai}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - flagstat: type: file description: File containing samtools flagstat output pattern: "*.{flagstat}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh"