nf-core_modules/software/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
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"
- 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"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@andersgs"
- "@drpatelh"