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
      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: 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"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@andersgs"
  - "@drpatelh"
