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

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name: ivar_consensus
description: Generate a consensus sequence from a BAM file using iVar
keywords:
- amplicon sequencing
- consensus
- fasta
tools:
- ivar:
description: |
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iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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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:
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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"
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- mpileup:
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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"