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102 lines
3.1 KiB
YAML
102 lines
3.1 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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- pdf:
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type: file
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description: File with plot of copy numbers or segments on chromosomes
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pattern: "*.{pdf}"
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- png:
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type: file
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description: File with plot of bin-level log2 coverages and segmentation calls
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pattern: "*.{png}"
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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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- "@SusiJo"
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