nf-core_modules/modules/ivar/variants/meta.yml
Matthias Hörtenhuber e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00

56 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
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: 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"
- save_mpileup:
type: boolean
description: Save mpileup file generated by ivar variants
patter: "*.mpileup"
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"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@andersgs"
- "@drpatelh"