name: ivar_consensus
description: Generate a consensus sequence from a BAM file using iVar
keywords:
    - amplicon sequencing
    - consensus
    - 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
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
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"
    - ref:
        type: file
        description: The reference sequence used for mapping and generating the BAM file
        pattern: "*.fa"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: iVar generated consensus sequence
        pattern: "*.fa"
    - qual:
        type: file
        description: iVar generated quality file
        pattern: "*.qual.txt"
    - mpileup:
        type: file
        description: mpileup output from samtools mpileup [OPTIONAL]
        pattern: "*.mpileup"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@andersgs"
    - "@drpatelh"