Nextflow Registry | nf-core/plastid/psite@0.0.0-0c7146d

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

Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length

genomics riboseq psite

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @suhrig

Maintainers: @suhrig

Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length

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

include { PLASTID_PSITE } from 'nf-core/plastid/psite'

MIT License

Process

`Name`	`PLASTID_PSITE`

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`

#2 tuple

`meta2` map	Map containing reference information for the reference genome GTF file e.g. `[ id:'Ensembl human v.111' ]`
`rois_txt` file	Tab-delimited text file describing the maximal spanning window for each gene (output from plastid_metagene_generate) `*.txt`

Output 4 channels

#1 versions

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

#2 p_offsets tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_p_offsets.txt` file	Selected p-site offset for each read length `*_p_offsets.txt`

#3 p_offsets_png tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_p_offsets.png` file	Graphical illustration of metagene profiles `*_p_offsets.png`

#4 metagene_profiles tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_metagene_profiles.txt` file	Matrix containing metagene profile for each read length `*_metagene_profiles.txt`

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 19:03:29 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplastid%2Fpsite/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plastid/psite/blobs/sha256:e2b4e8616814f0750493434b2d728293533a1444fe89bbdbacc2caa9b472ab40
Size	2.7 KB
Checksum	sha256:e2b4e8616814f0750493434b2d728293533a1444fe89bbdbacc2caa9b472ab40
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:03:29 (UTC)		1	2.7 KB	-