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

nf-core/phantompeakqualtools @ 0.0.0-0c7146d

"This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."

ChIP-Seq QC phantom peaks

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @drpatelh @edmundmiller @JoseEspinosa

Maintainers: @drpatelh @edmundmiller @JoseEspinosa

Summary

Get started

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

include { PHANTOMPEAKQUALTOOLS } from 'nf-core/phantompeakqualtools'

License

MIT License

Process

`Name`	`PHANTOMPEAKQUALTOOLS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`

Output 4 channels

#1 pdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pdf` file	A pdf containing save cross-correlation plots `*.{pdf}`

#2 spp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.out` file	A ChIP-Seq Processing Pipeline file containing peakshift/phantomPeak results `*.{out}`

#3 rdata tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.Rdata` file	Rdata file containing the R session `*.{Rdata}`

#4 versions

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

Tool	Description	Homepage
phantompeakqualtools	"This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."	n/a

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:25:02 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fphantompeakqualtools/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/phantompeakqualtools/blobs/sha256:cd82646f5d06f60926201a8379e62ee7c3e4a1f2efc9709d99c630a92c73a071
Size	2.9 KB
Checksum	sha256:cd82646f5d06f60926201a8379e62ee7c3e4a1f2efc9709d99c630a92c73a071
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:35:37 (UTC)		3	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:25:02 (UTC)		3	2.9 KB