mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
1455498152
* Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
93 lines
2.9 KiB
YAML
93 lines
2.9 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}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@kaurravneet4123"
|
|
- "@KevinMenden"
|
|
- "@MaxUlysse"
|
|
- "@drpatelh"
|
|
- "@fbdtemme"
|
|
- "@lassefolkersen"
|