mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
59 lines
1.9 KiB
YAML
59 lines
1.9 KiB
YAML
|
name: "scramble_clusteranalysis"
|
||
|
|
description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier`
|
||
|
|
keywords:
|
||
|
|
- soft-clipped clusters
|
||
|
|
- scramble
|
||
|
|
tools:
|
||
|
|
- "scramble":
|
||
|
|
description: "Soft Clipped Read Alignment Mapper"
|
||
|
|
homepage: "https://github.com/GeneDx/scramble"
|
||
|
|
documentation: "https://github.com/GeneDx/scramble"
|
||
|
|
tool_dev_url: "https://github.com/GeneDx/scramble"
|
||
|
|
doi: ""
|
||
|
|
licence: "['CC']"
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- clusters:
|
||
|
|
type: file
|
||
|
|
description: Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier
|
||
|
|
pattern: "*clusters.txt"
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.
|
||
|
|
pattern: "*.{fasta,fa}"
|
||
|
|
- mei_ref:
|
||
|
|
type: file
|
||
|
|
description: Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct
|
||
|
|
pattern: "*.{fasta,fa}"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
- meis_tab:
|
||
|
|
type: file
|
||
|
|
description: Tab-delimited text file containing MEI calls
|
||
|
|
pattern: "*_MEIs.txt"
|
||
|
|
- dels_tab:
|
||
|
|
type: file
|
||
|
|
description: Tab-delimited text file containing predicted deletions
|
||
|
|
pattern: "*_PredictedDeletions.txt"
|
||
|
|
- vcf:
|
||
|
|
type: file
|
||
|
|
description: A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)
|
||
|
|
pattern: "*.vcf"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@nvnieuwk"
|