mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
81 lines
2.4 KiB
YAML
81 lines
2.4 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"]
|
|
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 (only needed for cram_input and/or when normal_samples are provided)
|
|
- 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"
|