name: "samtools_markdup"
description: mark duplicate alignments in a coordinate sorted file
keywords:
  - markdup
tools:
  - "samtools":
      description: "Tools for dealing with SAM, BAM and CRAM files"
      homepage: "http://www.htslib.org"
      documentation: "https://www.htslib.org/doc/samtools-markdup.html"
      tool_dev_url: "https://github.com/samtools/samtools"
      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}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - output:
      type: file
      description: Sorted BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"

authors:
  - "@priyanka-surana"