name: samtools_merge
description: Merge BAM or CRAM file
keywords:
  - merge
  - 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 ]
  - input_files:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram,sam}"
  - fasta:
      type: optional file
      description: Reference file the CRAM was created with
      pattern: "*.{fasta,fa}"
  - fai:
      type: optional file
      description: Index of the reference file the CRAM was created with
      pattern: "*.fai"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.{bam}"
  - cram:
      type: file
      description: CRAM file
      pattern: "*.{cram}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - csi:
      type: file
      description: BAM index file (optional)
      pattern: "*.csi"
authors:
  - "@drpatelh"
  - "@yuukiiwa "
  - "@maxulysse"
  - "@FriederikeHanssen"