mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
87 lines
2.6 KiB
YAML
Executable file
87 lines
2.6 KiB
YAML
Executable file
name: cnvkit
|
|
description: Copy number variant detection from high-throughput sequencing data
|
|
keywords:
|
|
- bam
|
|
- fasta
|
|
- copy number
|
|
tools:
|
|
- cnvkit:
|
|
description: |
|
|
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
|
|
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
|
documentation: https://cnvkit.readthedocs.io/en/stable/index.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 ]
|
|
- tumourbam:
|
|
type: file
|
|
description: |
|
|
Input tumour sample bam file
|
|
- normalbam:
|
|
type: file
|
|
description: |
|
|
Input normal sample bam file
|
|
- fasta:
|
|
type: file
|
|
description: |
|
|
Input reference genome fasta file
|
|
- targetfile:
|
|
type: file
|
|
description: |
|
|
Input target bed file
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bed:
|
|
type: file
|
|
description: File containing genomic regions
|
|
pattern: "*.{bed}"
|
|
- cnn:
|
|
type: file
|
|
description: File containing coverage information
|
|
pattern: "*.{cnn}"
|
|
- cnr:
|
|
type: file
|
|
description: File containing copy number ratio information
|
|
pattern: "*.{cnr}"
|
|
- cns:
|
|
type: file
|
|
description: File containing copy number segment information
|
|
pattern: "*.{cns}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@kaurravneet4123"
|
|
- "@KevinMenden"
|
|
- "@MaxUlysse"
|
|
- "@drpatelh"
|
|
|