nf-core_modules/modules/ivar/variants/meta.yml

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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
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"
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- 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"
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output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
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- tsv:
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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:
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type: file
description: File containing software versions
pattern: "versions.yml"
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authors:
- "@andersgs"
- "@drpatelh"