modules/tobias_scorebigwig

Calculate ATAC-seq footprint scores from a BigWig signal track with TOBIAS ScoreBigwig

ATAC-seqfootprintingbigWigtranscription factors

https://github.com/nf-core/modules/[...]/modules/nf-core/tobias/scorebigwig

Description

Calculate ATAC-seq footprint scores from a BigWig signal track with TOBIAS ScoreBigwig

Input

name:type

description

pattern

`meta`
`:map`

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

`signal`
`:file`

BigWig ATAC-seq cut-site signal, typically generated by TOBIAS ATACorrect

*.bw

`regions`
`:file`

BED file containing genomic regions for footprint scoring

*.bed

Output

name:type

description

pattern

`footprints`

`meta`
`:map`

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

`*_footprints.bw`
`:file`

BigWig track containing TOBIAS footprint scores

*_footprints.bw

`versions_tobias`

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

The name of the process

`tobias`
`:string`

The name of the tool

`TOBIAS --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

`tobias`
`:string`

The name of the tool

`TOBIAS --version`
`:eval`

The expression to obtain the version of the tool

Tools

tobias
MIT

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

github.com/loosolab/TOBIAS github.com/loosolab/TOBIAS/wiki https://github.com/loosolab/TOBIAS 10.1038/s41467-020-18035-1

modules/tobias_scorebigwig

Description

Input

`meta`
`:map`

`signal`
`:file`

`regions`
`:file`

Output

`footprints`

`meta`
`:map`

`*_footprints.bw`
`:file`

`versions_tobias`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

Topics

`versions`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

Tools

tobias
MIT

maintainer

get in touch

modules/tobias_scorebigwig

Description

Input

meta :map

signal :file

regions :file

Output

footprints

meta :map

*_footprints.bw :file

versions_tobias

${task.process} :string

tobias :string

TOBIAS --version :eval

Topics

versions

${task.process} :string

tobias :string

TOBIAS --version :eval

Tools

tobiasMIT

maintainer

get in touch

`meta`
`:map`

`signal`
`:file`

`regions`
`:file`

`footprints`

`meta`
`:map`

`*_footprints.bw`
`:file`

`versions_tobias`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

`versions`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

tobias
MIT