name: ivar_trim
description: Trim primer sequences rom a BAM file with iVar
keywords:
    - amplicon sequencing
    - trimming
    - fasta
tools:
    - ivar:
        description: |
            iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
        homepage: https://github.com/andersen-lab/ivar
        documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bam:
        type: file
        description: Co-ordinate sorted BAM file
        pattern: "*.bam"
    - bai:
        type: file
        description: Index file for co-ordinate sorted BAM file
        pattern: "*.bai"
    - bed:
        type: file
        description: BED file with primer labels and positions
        pattern: "*.bed"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bam:
        type: file
        description: iVar generated trimmed bam file (unsorted)
        pattern: "*.bam"
    - log:
        type: file
        description: Log file generated by iVar for use with MultiQC
        pattern: "*.log"
    - version:
        type: file
        description: File containing software version
        pattern: "versions.yml"
authors:
    - "@andersgs"
    - "@drpatelh"