modules/tobias_bindetect

Estimate transcription factor binding and differential binding from ATAC-seq footprint BigWig tracks with TOBIAS BINDetect

ATAC-seqfootprintingtranscription factorsdifferential binding

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

Description

Estimate transcription factor binding and differential binding from ATAC-seq footprint BigWig tracks with TOBIAS BINDetect

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`signals`
`:file`

One or more BigWig tracks containing TOBIAS footprint scores, one per condition or sample

*.bw

`peaks`
`:file`

BED file containing the consensus open-chromatin regions

*.bed

`motifs`
`:file`

One or more transcription factor motif files in supported TOBIAS formats

*

`fasta`
`:file`

Reference genome FASTA file

*.{fa,fasta,fna}

Output

name:type

description

pattern

`outdir`

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`bindetect`
`:directory`

Complete TOBIAS BINDetect output directory, including motif-specific results

bindetect

`results`

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`bindetect/*_results.txt`
`:file`

Tab-delimited global transcription factor binding results

*_results.txt

`results_xlsx`

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`bindetect/*_results.xlsx`
`:file`

Excel global transcription factor binding results

*_results.xlsx

`distances`

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`bindetect/*_distances.txt`
`:file`

Transcription factor motif-distance summary table

*_distances.txt

`figures`

`meta`
`:map`

Groovy Map containing analysis information e.g. [ id:'all_samples' ]

`bindetect/*_figures.pdf`
`:file`

TOBIAS BINDetect summary figure PDF

*_figures.pdf

`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_bindetect

Description

Input

`meta`
`:map`

`signals`
`:file`

`peaks`
`:file`

`motifs`
`:file`

`fasta`
`:file`

Output

`outdir`

`meta`
`:map`

`bindetect`
`:directory`

`results`

`meta`
`:map`

`bindetect/*_results.txt`
`:file`

`results_xlsx`

`meta`
`:map`

`bindetect/*_results.xlsx`
`:file`

`distances`

`meta`
`:map`

`bindetect/*_distances.txt`
`:file`

`figures`

`meta`
`:map`

`bindetect/*_figures.pdf`
`: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_bindetect

Description

Input

meta :map

signals :file

peaks :file

motifs :file

fasta :file

Output

outdir

meta :map

bindetect :directory

results

meta :map

bindetect/*_results.txt :file

results_xlsx

meta :map

bindetect/*_results.xlsx :file

distances

meta :map

bindetect/*_distances.txt :file

figures

meta :map

bindetect/*_figures.pdf :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`

`signals`
`:file`

`peaks`
`:file`

`motifs`
`:file`

`fasta`
`:file`

`outdir`

`meta`
`:map`

`bindetect`
`:directory`

`results`

`meta`
`:map`

`bindetect/*_results.txt`
`:file`

`results_xlsx`

`meta`
`:map`

`bindetect/*_results.xlsx`
`:file`

`distances`

`meta`
`:map`

`bindetect/*_distances.txt`
`:file`

`figures`

`meta`
`:map`

`bindetect/*_figures.pdf`
`:file`

`versions_tobias`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

`versions`

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

`tobias`
`:string`

`TOBIAS --version`
`:eval`

tobias
MIT