mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
51 lines
1.7 KiB
YAML
51 lines
1.7 KiB
YAML
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"
|
|
- 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"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- tsv:
|
|
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: "versions.yml"
|
|
authors:
|
|
- "@andersgs"
|
|
- "@drpatelh"
|