Nextflow Registry | nf-core/plastid/make

nf-core/plastid/make_wiggle @ 0.0.0-0c7146d

Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser

genomics riboseq psite wiggle bedgraph

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @suhrig

Maintainers: @suhrig

Summary

Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser

Get started

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

include { PLASTID_MAKE_WIGGLE } from 'nf-core/plastid/make_wiggle'

License

MIT License

Process

`Name`	`PLASTID_MAKE_WIGGLE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bam` file	Genome BAM file `*.bam`
`bam_index` file	Genome BAM index file `*.bai`
`p_offsets` file	Selected p-site offset for each read length (output from plastid_psite). Required when mapping_rule is 'fiveprime_variable', otherwise pass empty list []. `*_p_offsets.txt`

`mapping_rule` string	Read mapping rule. Use 'fiveprime_variable' with p_offsets file to map reads to P-sites.

Output 2 channels

#1 tracks tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.{wig,bedgraph}` file	wig/bedgraph tracks for forward and reverse strands `*.{wig,bedgraph}`

#2 versions

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

Tool	Description	Homepage
plastid	Nucleotide-resolution analysis of next-generation sequencing and genomics data	https://github.com/joshuagryphon/plastid

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:03:26 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplastid%2Fmake_wiggle/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plastid/make_wiggle/blobs/sha256:14a33be2b9c120f9fd17f074d6df42579a4d2449095d3ca021a2c87f616362cb
Size	2.8 KB
Checksum	sha256:14a33be2b9c120f9fd17f074d6df42579a4d2449095d3ca021a2c87f616362cb
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:03:26 (UTC)		1	2.8 KB	-