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https://github.com/MillironX/nf-core_modules.git
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59 lines
1.9 KiB
YAML
59 lines
1.9 KiB
YAML
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name: "scramble_clusteranalysis"
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description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier`
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keywords:
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- soft-clipped clusters
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- scramble
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tools:
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- "scramble":
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description: "Soft Clipped Read Alignment Mapper"
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homepage: "https://github.com/GeneDx/scramble"
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documentation: "https://github.com/GeneDx/scramble"
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tool_dev_url: "https://github.com/GeneDx/scramble"
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doi: ""
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licence: "['CC']"
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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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- clusters:
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type: file
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description: Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier
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pattern: "*clusters.txt"
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- fasta:
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type: file
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description: Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.
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pattern: "*.{fasta,fa}"
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- mei_ref:
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type: file
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description: Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct
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pattern: "*.{fasta,fa}"
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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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- 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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- meis_tab:
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type: file
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description: Tab-delimited text file containing MEI calls
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pattern: "*_MEIs.txt"
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- dels_tab:
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type: file
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description: Tab-delimited text file containing predicted deletions
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pattern: "*_PredictedDeletions.txt"
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- vcf:
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type: file
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description: A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)
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pattern: "*.vcf"
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authors:
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- "@nvnieuwk"
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