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}

meta:map

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

ipbai:file

BAM index

*.{bai}

controlbai:file

BAM index

*.{bai}

meta2: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 ]

${crosslinks_output_name}:file

Bed file of crosslinks

*.{bed}

peaks

meta:map

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

${peaks_output_name}:file

Bed file of peaks

*.{bed}

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user charlotteanne
Github user marcjones
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