name: fgbio_callmolecularconsensusreads
description: Calls consensus sequences from reads with the same unique molecular tag.

keywords:
    - UMIs
    - consensus sequence
    - bam
    - sam
tools:
    - fgbio:
        description: Tools for working with genomic and high throughput sequencing data.
        homepage: https://github.com/fulcrumgenomics/fgbio
        documentation: http://fulcrumgenomics.github.io/fgbio/
        licence: ['MIT']

input:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false, collapse:false ]
    - bam:
        type: file
        description: |
          The input SAM or BAM file.
        pattern: "*.{bam,sam}"

output:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - bam:
        type: file
        description: |
          Output SAM or BAM file to write consensus reads.
        pattern: "*.{bam,sam}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"

authors:
    - "@sruthipsuresh"