name: samtools_idxstats
description: Reports alignment summary statistics for a BAM/CRAM/SAM file
keywords:
  - stats
  - mapping
  - counts
  - chromosome
  - 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: http://www.htslib.org/doc/samtools.html
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]
      identifier: biotools:samtools
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}"
        ontologies: []
    - bai:
        type: file
        description: Index for BAM/CRAM/SAM file
        pattern: "*.{bai,crai,sai}"
        ontologies: []
output:
  idxstats:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.idxstats":
          type: file
          description: File containing samtools idxstats output
          pattern: "*.{idxstats}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@drpatelh"
maintainers:
  - "@drpatelh"
