mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
72 lines
2.4 KiB
YAML
72 lines
2.4 KiB
YAML
name: ivar_consensus
|
|
description: Generate a consensus sequence from a BAM file using iVar
|
|
keywords:
|
|
- amplicon sequencing
|
|
- consensus
|
|
- 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"
|
|
- ref:
|
|
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"
|
|
- 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"
|