modules/scramble_clusteranalysis

The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier

soft-clipped clustersscramblecluster analysisclusteridentifier

https://github.com/nf-core/modules/[...]/modules/nf-core/scramble/clusteranalysis

Description

The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`clusters`
`:file`

Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier

*clusters.txt

`meta2`
`:map`

Groovy Map containing information about the fasta file e.g. [ id:‘test’ ]

`fasta`
`:file`

The reference FASTA file (mandatory when using CRAM files)

*.{fasta,fa}

`mei_ref`
`:file`

Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn’t correct

*.{fasta,fa}

Output

name:type

description

pattern

`meis_tab`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*_MEIs.txt`
`:file`

Tab-delimited text file containing MEI calls

*_MEIs.txt

`dels_tab`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*_PredictedDeletions.txt`
`:file`

Tab-delimited text file containing predicted deletions

*_PredictedDeletions.txt

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.vcf`
`:file`

A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)

*.vcf

`versions_scramble`

`${task.process}`
`:string`

The process the versions were collected from

`scramble`
`:string`

The tool name

`1.0.2`
`:string`

The version of the tool (hardcoded, not available via CLI)

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`scramble`
`:string`

The tool name

`1.0.2`
`:string`

The version of the tool (hardcoded, not available via CLI)

Tools

scramble
CC

Soft Clipped Read Alignment Mapper

github.com/GeneDx/scramble

modules/scramble_clusteranalysis

Description

Input

`meta`
`:map`

`clusters`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`mei_ref`
`:file`

Output

`meis_tab`

`meta`
`:map`

`*_MEIs.txt`
`:file`

`dels_tab`

`meta`
`:map`

`*_PredictedDeletions.txt`
`:file`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_scramble`

`${task.process}`
`:string`

`scramble`
`:string`

`1.0.2`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`scramble`
`:string`

`1.0.2`
`:string`

Tools

scramble
CC

maintainer

get in touch

modules/scramble_clusteranalysis

Description

Input

meta :map

clusters :file

meta2 :map

fasta :file

mei_ref :file

Output

meis_tab

meta :map

*_MEIs.txt :file

dels_tab

meta :map

*_PredictedDeletions.txt :file

vcf

meta :map

*.vcf :file

versions_scramble

${task.process} :string

scramble :string

1.0.2 :string

Topics

versions

${task.process} :string

scramble :string

1.0.2 :string

Tools

scrambleCC

maintainer

get in touch

`meta`
`:map`

`clusters`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`mei_ref`
`:file`

`meis_tab`

`meta`
`:map`

`*_MEIs.txt`
`:file`

`dels_tab`

`meta`
`:map`

`*_PredictedDeletions.txt`
`:file`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_scramble`

`${task.process}`
`:string`

`scramble`
`:string`

`1.0.2`
`:string`

`versions`

`${task.process}`
`:string`

`scramble`
`:string`

`1.0.2`
`:string`

scramble
CC