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

nf-core/plotsr @ 0.0.0-0c7146d

Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes.

genomics synteny rearrangements chromosome

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GallVp

Maintainers: @GallVp

Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes.

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

include { PLOTSR } from 'nf-core/plotsr'

MIT License

Process

`Name`	`PLOTSR`

Input 8 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`syri` file	Structural annotation mappings (syri.out) identified by SyRI `*syri.out`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`fastas` list	Fasta files in the sequence specified by the `genomes` file `*.{fasta,fa,fsa,faa}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`genomes` string	A genomes.txt file including the header: #file name tags and Fasta file names, title for the plot and plotsr configuration tags. As example is: #file name tags genome.fasta test lw:1.5 genome2.fasta reference lw:1.5 `*.txt`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bedpe` file	Structural annotation mappings in BEDPE format `*.bedpe`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`markers` file	File containing path to markers `*.bed`

#6 tuple

`meta6` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`tracks` file	File listing paths and details for all tracks to be plotted `*.txt`

#7 tuple

`meta7` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`chrord` file	File containing reference (first genome) chromosome IDs in the order in which they are to be plotted. File requires one chromosome ID per line. Not compatible with --chr `*.txt`

#8 tuple

`meta8` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`chrname` file	File containing reference (first genome) chromosome names to be used in the plot. File needs to be a TSV with the chromosome ID in first column and chromosome name in the second. `*.txt`

Output 2 channels

#1 png tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.png` file	Synteny plot `*.png`

#2 versions

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

Tool	Description	Homepage
plotsr	Visualiser for structural annotations between multiple genomes	https://github.com/schneebergerlab/plotsr

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:04:42 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplotsr/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plotsr/blobs/sha256:2705ac01e3680e20a42972b1b324ba2c60ca5d2f16647c0feab1ed0babc6004c