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https://github.com/MillironX/nf-core_modules.git
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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
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description: Copy number variant detection from high-throughput sequencing data
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keywords:
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- bam
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- fasta
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- copy number
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tools:
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- cnvkit:
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description: |
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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.
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homepage: https://cnvkit.readthedocs.io/en/stable/index.html
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documentation: https://cnvkit.readthedocs.io/en/stable/index.html
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licence: ['Apache-2.0']
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- tumour:
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type: file
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description: |
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Input tumour sample bam file (or cram)
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- normal:
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type: file
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description: |
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Input normal sample bam file (or cram)
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- fasta:
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type: file
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description: |
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Input reference genome fasta file
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- targetfile:
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type: file
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description: |
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Input target bed file
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- reference:
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type: file
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description: |
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Input reference cnn-file (only for germline and tumor-only running)
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bed:
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type: file
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description: File containing genomic regions
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pattern: "*.{bed}"
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- cnn:
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type: file
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description: File containing coverage information
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pattern: "*.{cnn}"
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- cnr:
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type: file
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description: File containing copy number ratio information
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pattern: "*.{cnr}"
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- cns:
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type: file
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description: File containing copy number segment information
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pattern: "*.{cns}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@kaurravneet4123"
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- "@KevinMenden"
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- "@MaxUlysse"
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- "@drpatelh"
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- "@fbdtemme"
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- "@lassefolkersen"
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