nf-core_modules/modules/cnvkit/batch/meta.yml
2022-05-20 09:12:47 +02:00

102 lines
3.1 KiB
YAML

name: cnvkit_batch
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
licence: ["Apache-2.0"]
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 ]
- tumour:
type: file
description: |
Input tumour sample bam file (or cram)
- normal:
type: file
description: |
Input normal sample bam file (or cram)
- fasta:
type: file
description: |
Input reference genome fasta file
- targetfile:
type: file
description: |
Input target bed file
- reference:
type: file
description: |
Input reference cnn-file (only for germline and tumor-only running)
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}"
- pdf:
type: file
description: File with plot of copy numbers or segments on chromosomes
pattern: "*.{pdf}"
- png:
type: file
description: File with plot of bin-level log2 coverages and segmentation calls
pattern: "*.{png}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@kaurravneet4123"
- "@KevinMenden"
- "@MaxUlysse"
- "@drpatelh"
- "@fbdtemme"
- "@lassefolkersen"
- "@SusiJo"