Nextflow Registry | nf-core/pureclip@0.0.0-0c7146d

nf-core/pureclip @ 0.0.0-0c7146d

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

iCLIP eCLIP CLIP

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @charlotteanne @marcjones

Maintainers: @charlotteanne @marcjones

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

Add the following snippet to your workflow script to include this module.

include { PURECLIP } from 'nf-core/pureclip'

MIT License

Process

`Name`	`PURECLIP`

Input 4 channels

#1 tuple

`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}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`ipbai` file	BAM index `*.{bai}`
`controlbai` file	BAM index `*.{bai}`

#3 tuple

`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 3 channels

#1 peaks tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`${peaks_output_name}` file	Bed file of peaks `*.{bed}`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 crosslinks tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`${crosslinks_output_name}` file	Bed file of crosslinks `*.{bed}`

Tool	Description	Homepage
pureclip	PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.	https://github.com/skrakau/PureCLIP

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:28:52 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpureclip/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pureclip/blobs/sha256:a93156f69c13fae4c62672888682abb220cd0314f0343a463c2802ef2e76a8b3
Size	2.7 KB
Checksum	sha256:a93156f69c13fae4c62672888682abb220cd0314f0343a463c2802ef2e76a8b3
Downloads	4

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:38:44 (UTC)	3	2.8 KB
0.0.0-3fc6d40	22 Apr 2026 15:27:41 (UTC)	4	2.8 KB
0.0.0-0c7146d	08 Apr 2026 19:28:52 (UTC)	4	2.7 KB