name: samtools_view
description: filter/convert SAM/BAM/CRAM file
keywords:
  - view
  - 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"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - index:
      type: file
      description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional)
      pattern: "*.{.bai,.csi,.crai}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Reference file the CRAM was created with (optional)
      pattern: "*.{fasta,fa}"
  - qname:
      type: file
      description: Optional file with read names to output only select alignments
      pattern: "*.{txt,list}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: optional filtered/converted BAM file
      pattern: "*.{bam}"
  - cram:
      type: file
      description: optional filtered/converted CRAM file
      pattern: "*.{cram}"
  - sam:
      type: file
      description: optional filtered/converted SAM file
      pattern: "*.{sam}"
  # bai, csi, and crai are created with `--write-index`
  - bai:
      type: file
      description: optional BAM file index
      pattern: "*.{bai}"
  - csi:
      type: file
      description: optional tabix BAM file index
      pattern: "*.{csi}"
  - crai:
      type: file
      description: optional CRAM file index
      pattern: "*.{crai}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@joseespinosa"
  - "@FriederikeHanssen"
  - "@priyanka-surana"
