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72 lines
2.1 KiB
YAML
72 lines
2.1 KiB
YAML
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name: tiddit_sv
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description: Identify chromosomal rearrangements.
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keywords:
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- structural
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- variants
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- vcf
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tools:
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- sv:
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description: Search for structural variants.
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homepage: https://github.com/SciLifeLab/TIDDIT
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documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
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doi: 10.12688/f1000research.11168.1
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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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- fasta:
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type: file
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description: Input FASTA file
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pattern: "*.{fasta,fa}"
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- fai:
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type: file
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description: FASTA index file
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pattern: "*.{fai}"
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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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- vcf:
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type: file
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description: vcf
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pattern: "*.{vcf}"
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- ploidy:
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type: file
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description: tab
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pattern: "*.{ploidy.tab}"
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- signals:
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type: file
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description: tab
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pattern: "*.{signals.tab}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@maxulysse"
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