cellgeni/irods/getmetadata @ 1.0.0

Module to get metadata from an iRODS collections and data objects and output as CSV

irods metadata csv

Latest version: 1.0.0

Total downloads: 3

Authors: @claptar

Maintainers: @claptar

cellgeni/irods/getmetadata

Summary

Extract metadata for an iRODS collection or data object and write the result to a CSV file.

The module checks whether the supplied iRODS path is a collection or a data object, runs imeta ls on the appropriate target, and formats the returned attribute/value/unit fields into irods_metadata.csv.

Get started

Include this module in your Nextflow pipeline:

include { IRODS_GETMETADATA } from 'cellgeni/irods/getmetadata'

Usage

Inputs

Input	Type	Description
`tuple val(meta), val(irodspath)`	map, string	Sample metadata and the iRODS collection or data object path to inspect.

Outputs

Output	Type	Description
`tuple val(meta), path("irods_metadata.csv")`	map, file	CSV file containing iRODS metadata.
`path("versions.yml")`	file	Software versions used by the module.

Dependencies

The module expects the following iRODS command-line tools to be available in the execution environment:

ils
imeta
ienv

License

MIT

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`irodspath` string	iRODS collection or data object path to get metadata from

Output 2 channels

#1 meta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`irods_metadata.csv` file	CSV file containing iRODS metadata `irods_metadata.csv`

#2 versions

`versions` file	YAML file containing software versions used `versions.yml`

Tool	Description	Homepage
irods	Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow.	https://irods.org/

Version	1.0.0
Release Date	29 Apr 2026 12:59:01 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/cellgeni%2Firods%2Fgetmetadata/1.0.0/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/cellgeni/irods/getmetadata/blobs/sha256:2585872ba144ef8d839152f93ded0807011d710930759b21b8d99b68f8a4bb5e
Size	2.7 KB
Checksum	sha256:2585872ba144ef8d839152f93ded0807011d710930759b21b8d99b68f8a4bb5e
Downloads	3

Version	Date	Status	Downloads	Size
1.0.0	29 Apr 2026 12:59:01 (UTC)		3	2.7 KB