modules/pints_caller

Main caller script for peak calling

peak-callingCoPROGRO-capPRO-capCAGENETCAGERAMPAGEcsRNA-seqSTRIPE-seqPRO-seqGRO-seq

https://github.com/nf-core/modules/[...]/modules/nf-core/pints/caller

Description

Main caller script for peak calling

Input

name:type

description

pattern

`meta`
`:map`

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

`bams`
`:file`

One or more BAM files

*.{bam}

`bais`
`:file`

Corresponding BAM file indexes

*.bam.bai

`assay_type`
`:string`

Assay type

Output

name:type

description

pattern

`divergent_TREs`

`meta`
`:map`

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

`*_divergent_peaks.bed`
`:file`

Divergent TREs

*_divergent_peaks.bed

`bidirectional_TREs`

`meta`
`:map`

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

`*_bidirectional_peaks.bed`
`:file`

Divergent TREs and convergent TREs

*_bidirectional_peaks.bed

`unidirectional_TREs`

`meta`
`:map`

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

`*_unidirectional_peaks.bed`
`:file`

Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs)

*_unidirectional_peaks.bed

`peakcalling_log`

`meta`
`:map`

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

`peakcalling_*.log`
`:file`

Peakcalling log for debugging purposes

peakcalling_*.log

`versions_pints`

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

The name of the process

`pints`
`:string`

The name of the tool

`pints_caller --version`
`:eval`

The expression to obtain the version of the tool

`versions_python`

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

The name of the process

`python`
`:string`

The name of the tool

`python --version | sed 's/Python //g'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pints`
`:string`

The name of the tool

`pints_caller --version`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`python`
`:string`

The name of the tool

`python --version | sed 's/Python //g'`
`:eval`

The expression to obtain the version of the tool

Tools

pints
GPL v3

Peak Identifier for Nascent Transcripts Starts (PINTS)

pints.yulab.org github.com/hyulab/PINTS/blob/main/README.md https://github.com/hyulab/PINTS 10.1038/s41587-022-01211-7

modules/pints_caller

Description

Input

`meta`
`:map`

`bams`
`:file`

`bais`
`:file`

`assay_type`
`:string`

Output

`divergent_TREs`

`meta`
`:map`

`*_divergent_peaks.bed`
`:file`

`bidirectional_TREs`

`meta`
`:map`

`*_bidirectional_peaks.bed`
`:file`

`unidirectional_TREs`

`meta`
`:map`

`*_unidirectional_peaks.bed`
`:file`

`peakcalling_log`

`meta`
`:map`

`peakcalling_*.log`
`:file`

`versions_pints`

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

`pints`
`:string`

`pints_caller --version`
`:eval`

`versions_python`

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

`python`
`:string`

`python --version | sed 's/Python //g'`
`:eval`

Topics

`versions`

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

`pints`
`:string`

`pints_caller --version`
`:eval`

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

`python`
`:string`

`python --version | sed 's/Python //g'`
`:eval`

Tools

pints
GPL v3

maintainer

get in touch

modules/pints_caller

Description

Input

meta :map

bams :file

bais :file

assay_type :string

Output

divergent_TREs

meta :map

*_divergent_peaks.bed :file

bidirectional_TREs

meta :map

*_bidirectional_peaks.bed :file

unidirectional_TREs

meta :map

*_unidirectional_peaks.bed :file

peakcalling_log

meta :map

peakcalling_*.log :file

versions_pints

${task.process} :string

pints :string

pints_caller --version :eval

versions_python

${task.process} :string

python :string

python --version | sed 's/Python //g' :eval

Topics

versions

${task.process} :string

pints :string

pints_caller --version :eval

${task.process} :string

python :string

python --version | sed 's/Python //g' :eval

Tools

pintsGPL v3

maintainer

get in touch

`meta`
`:map`

`bams`
`:file`

`bais`
`:file`

`assay_type`
`:string`

`divergent_TREs`

`meta`
`:map`

`*_divergent_peaks.bed`
`:file`

`bidirectional_TREs`

`meta`
`:map`

`*_bidirectional_peaks.bed`
`:file`

`unidirectional_TREs`

`meta`
`:map`

`*_unidirectional_peaks.bed`
`:file`

`peakcalling_log`

`meta`
`:map`

`peakcalling_*.log`
`:file`

`versions_pints`

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

`pints`
`:string`

`pints_caller --version`
`:eval`

`versions_python`

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

`python`
`:string`

`python --version | sed 's/Python //g'`
`:eval`

`versions`

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

`pints`
`:string`

`pints_caller --version`
`:eval`

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

`python`
`:string`

`python --version | sed 's/Python //g'`
`:eval`

pints
GPL v3