Nextflow Registry | nf-core/peka@0.0.0-6c4ed3a

nf-core/peka @ 0.0.0-6c4ed3a

Runs PEKA CLIP peak k-mer analysis

motif CLIP iCLIP genomics k-mer

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @kkuret @codeprimate123 @chris-cheshire @charlotteanne

Maintainers: @kkuret @codeprimate123 @chris-cheshire @charlotteanne

Runs PEKA CLIP peak k-mer analysis

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

include { PEKA } from 'nf-core/peka'

MIT License

Process

`Name`	`PEKA`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`peaks` file	BED file of peak regions `*.{bed,bed.gz}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`crosslinks` file	BED file of crosslinks `*.{bed,bed.gz}`

`fasta` file	Genome reference sequence used `*.{fa,fasta}`

`fai` file	FAI file corresponding to the reference sequence `*.{fai}`

`gtf` file	A segmented GTF used to annotate peaks `*.{gtf}`

Output 8 channels

#1 oxn tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`oxn.bed.gz` file	BED file of oxn sites `oxn.bed.gz`

#2 pdf tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`*.pdf` file	PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites `*.pdf`

#3 rtxn tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`rtxn` file	rtxn file `rtxn`

#4 clust tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`*_clusters.csv` file	CSV file of clusters `*_clusters.csv`

#5 tsites tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`thresholded_sites.bed.gz` file	BED file of thresholded sites `thresholded_sites.bed.gz`

#6 cluster tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`mer_cluster_distribution` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`

#7 versions

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

#8 distribution tuple

`meta` file	TSV file of summed occurrence distributions of k-mers within defined clusters `*.tsv`
`mer_distribution` file	TSV file with calculated PEKA score and occurrence distribution for all possible k-mers `*.tsv`

Tool	Description	Homepage
peka	Positionally-enriched k-mer analysis (PEKA) is a software package for identifying enriched protein-RNA binding motifs from CLIP datasets	https://github.com/ulelab/peka