name: ivar_variants
description: Call variants from a BAM file using iVar
keywords:
    - amplicon sequencing
    - variants
    - 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
        licence: ['GPL-3.0-or-later']
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - bam:
        type: file
        description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file
        pattern: "*.bam"
    - fasta:
        type: file
        description: The reference sequence used for mapping and generating the BAM file
        pattern: "*.fa"
    - gff:
        type: file
        description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
        patter: "*.gff"
    - save_mpileup:
        type: boolean
        description: Save mpileup file generated by ivar variants
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - tsv:
        type: file
        description: iVar generated TSV file with the variants
        pattern: "*.tsv"
    - mpileup:
        type: file
        description: mpileup output from samtools mpileup [OPTIONAL]
        pattern: "*.mpileup"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@andersgs"
    - "@drpatelh"