modules/juicertools_pre

Create a multi-resolution .hic contact matrix for analysis with Juicer

hiccontact mapgenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/juicertools/pre

Description

Create a multi-resolution .hic contact matrix for analysis with Juicer

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`pairs`
`:file`

Optionally gzipped TSV file, in one of a number of formats, including pairs format. See https://github.com/aidenlab/juicer/wiki/Pre#file-format for details.

*.{pairs,tsv}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`genome_id`
`:string`

String of a supported genome ID, see https://github.com/aidenlab/juicer/wiki/Pre#usage for details. Incompatible with chromsizes option.

`chromsizes`
`:file`

Headerless TSV file describing chromosome sizes with format: chrom_name\tlength

Incompatible with genome_id option.

*.{tsv}

Output

name:type

description

pattern

`hic`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.hic`
`:file`

.hic file for analysis and visualisation in Juicer

*.{hic}

`versions_juicertools`

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

The name of the process

`juicer_tools`
`:string`

The name of the tool

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`juicer_tools`
`:string`

The name of the tool

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

The expression to obtain the version of the tool

Tools

juicertools
MIT

Visualization and analysis software for Hi-C data

github.com/aidenlab/juicer 10.1016/j.cels.2016.07.002

modules/juicertools_pre

Description

Input

`meta`
`:map`

`pairs`
`:file`

`meta2`
`:map`

`genome_id`
`:string`

`chromsizes`
`:file`

Output

`hic`

`meta`
`:map`

`*.hic`
`:file`

`versions_juicertools`

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

`juicer_tools`
`:string`

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

Topics

`versions`

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

`juicer_tools`
`:string`

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

Tools

juicertools
MIT

maintainer

get in touch

modules/juicertools_pre

Description

Input

meta :map

pairs :file

meta2 :map

genome_id :string

chromsizes :file

Output

hic

meta :map

*.hic :file

versions_juicertools

${task.process} :string

juicer_tools :string

juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //" :eval

Topics

versions

${task.process} :string

juicer_tools :string

juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //" :eval

Tools

juicertoolsMIT

maintainer

get in touch

`meta`
`:map`

`pairs`
`:file`

`meta2`
`:map`

`genome_id`
`:string`

`chromsizes`
`:file`

`hic`

`meta`
`:map`

`*.hic`
`:file`

`versions_juicertools`

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

`juicer_tools`
`:string`

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

`versions`

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

`juicer_tools`
`:string`

`juicer_tools -V | grep "Version" | sed "s/Juicer Tools Version //"`
`:eval`

juicertools
MIT