Nextflow Registry | nf-core/plastid/make

nf-core/plastid/make_wiggle @ 0.0.0-3fc6d40

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: 0.0.0-6c4ed3a

Total downloads: 11

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:26:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fplastid%2Fmake_wiggle/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plastid/make_wiggle/blobs/sha256:3231cec45d32c284d4be5296e567fa8d371d303d0adb395d9a46e8b9a0ee580e
Size	2.8 KB
Checksum	sha256:3231cec45d32c284d4be5296e567fa8d371d303d0adb395d9a46e8b9a0ee580e
Downloads	5

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:37:34 (UTC)	3	2.8 KB
0.0.0-3fc6d40	22 Apr 2026 15:26:41 (UTC)	5	2.8 KB
0.0.0-0c7146d	08 Apr 2026 19:26:26 (UTC)	3	2.8 KB