modules/pureclip

PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

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

Description

PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

Input

name:type

description

pattern

`meta`
`:map`

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

`ipbam`
`:file`

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`controlbam`
`:file`

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`meta2`
`:map`

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

`ipbai`
`:file`

BAM index

*.{bai}

`controlbai`
`:file`

BAM index

*.{bai}

`meta3`
`:map`

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

`genome_fasta`
`:file`

FASTA file of reference genome

*.{fa,fasta,fa.gz,fasta.gz}

`input_control`
`:boolean`

Whether to run PureCLIP with an input control

Output

name:type

description

pattern

`crosslinks`

`meta`
`:map`

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

`${prefix}_pureclip_crosslinks.bed`
`:file`

Bed file of crosslinks

*.{bed}

`peaks`

`meta`
`:map`

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

`${prefix}_pureclip_peaks.bed`
`:file`

Bed file of peaks

*.{bed}

`versions_pureclip`

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

The name of the process

`pureclip`
`:string`

The name of the tool

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`pureclip`
`:string`

The name of the tool

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

pureclip
GPL v3

PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

github.com/skrakau/PureCLIP pureclip.readthedocs.io/en/latest/GettingStarted https://github.com/skrakau/PureCLIP 10.1186/s13059-017-1364-2

modules/pureclip

Description

Input

`meta`
`:map`

`ipbam`
`:file`

`controlbam`
`:file`

`meta2`
`:map`

`ipbai`
`:file`

`controlbai`
`:file`

`meta3`
`:map`

`genome_fasta`
`:file`

`input_control`
`:boolean`

Output

`crosslinks`

`meta`
`:map`

`${prefix}_pureclip_crosslinks.bed`
`:file`

`peaks`

`meta`
`:map`

`${prefix}_pureclip_peaks.bed`
`:file`

`versions_pureclip`

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

`pureclip`
`:string`

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

Topics

`versions`

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

`pureclip`
`:string`

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

Tools

pureclip
GPL v3

maintainers

get in touch

modules/pureclip

Description

Input

meta :map

ipbam :file

controlbam :file

meta2 :map

ipbai :file

controlbai :file

meta3 :map

genome_fasta :file

input_control :boolean

Output

crosslinks

meta :map

${prefix}_pureclip_crosslinks.bed :file

peaks

meta :map

${prefix}_pureclip_peaks.bed :file

versions_pureclip

${task.process} :string

pureclip :string

pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p' :eval

Topics

versions

${task.process} :string

pureclip :string

pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p' :eval

Tools

pureclipGPL v3

maintainers

get in touch

`meta`
`:map`

`ipbam`
`:file`

`controlbam`
`:file`

`meta2`
`:map`

`ipbai`
`:file`

`controlbai`
`:file`

`meta3`
`:map`

`genome_fasta`
`:file`

`input_control`
`:boolean`

`crosslinks`

`meta`
`:map`

`${prefix}_pureclip_crosslinks.bed`
`:file`

`peaks`

`meta`
`:map`

`${prefix}_pureclip_peaks.bed`
`:file`

`versions_pureclip`

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

`pureclip`
`:string`

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

`versions`

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

`pureclip`
`:string`

`pureclip --version 2>&1 | sed -n 's/^.*pureclip version: //p'`
`:eval`

pureclip
GPL v3