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"