nf-core_modules/modules/samtools/view/meta.yml

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: 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:
        type: file
        description: BAM/CRAM/SAM file
        pattern: "*.{bam,cram,sam}"
    - fasta:
        type: optional file
        description: Reference file the CRAM was created with
        pattern: "*.{fasta,fa}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bam:
        type: file
        description: filtered/converted BAM/SAM file
        pattern: "*.{bam,sam}"
    - cram:
        type: file
        description: filtered/converted CRAM file
        pattern: "*.cram"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@drpatelh"
    - "@joseespinosa"
    - "@FriederikeHanssen"