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meta.yml
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meta.yml
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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"