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: 0.0.0-6c4ed3a

Total downloads: 10

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:26:30 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fplastid%2Fpsite/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plastid/psite/blobs/sha256:9c82888026123e8871ef557cc7cdd611721127eef8c3570bd7795272780415bc
Size	2.6 KB
Checksum	sha256:9c82888026123e8871ef557cc7cdd611721127eef8c3570bd7795272780415bc
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:37:36 (UTC)	3	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:26:44 (UTC)	4	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:26:30 (UTC)	3	2.6 KB