cellgeni/irods/getfile @ 1.0.0

Downloads a file from iRODS to the local working directory and verifies its integrity by comparing the local MD5 checksum against the iRODS-recorded checksum.

iRODS download checksum md5

Latest version: 1.0.0

Total downloads: 1

Authors: @ab76

Maintainers: @ab76

cellgeni/irods/getfile

Summary

Downloads a file from iRODS to the local working directory and verifies its integrity by comparing the local MD5 checksum against the iRODS-recorded checksum. The process exits with an error if the file does not exist on iRODS or if the checksums do not match.

Inputs

Name	Type	Description
`meta.id`	string	Sample identifier.
`irodsfile`	string	Full iRODS path to the file to download (e.g. `/seq/illumina/runs/12345/12345_1#1.cram`).

Outputs

Name	File(s)	Description
`file`	`*`	The downloaded file in the task working directory.
`versions`	`versions.yml`	YAML file recording the versions of iRODS iCommands, awk, and md5sum.

Usage

include { IRODS_GETFILE } from 'cellgeni/irods/getfile'

IRODS_GETFILE(
    channel.of([[id: 'sample1'], '/seq/illumina/runs/12345/12345_1#1.cram'])
)

License

MIT

Input 1 channel

#1 tuple

`meta` map	Map with sample-level metadata. Must contain key 'id'. e.g. [ id:'sample1' ]
`irodsfile` string	Full iRODS path to the file to download (e.g. '/seq/illumina/runs/12345/12345_1#1.cram').

Output 2 channels

#1 file tuple

`meta` map	Map with sample-level metadata, passed through from input. e.g. [ id:'sample1' ]
`*` file	The downloaded file, placed in the task working directory.

#2 versions

Tool	Description	Homepage
iget	Downloads a data object from iRODS to the local filesystem.	https://docs.irods.org/master/icommands/user/#iget
ichksum	Computes and retrieves the checksum of an iRODS data object.	https://docs.irods.org/master/icommands/user/#ichksum

Version	1.0.0
Release Date	20 May 2026 15:30:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/cellgeni%2Firods%2Fgetfile/1.0.0/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/cellgeni/irods/getfile/blobs/sha256:664784ecdc8c056cbd55fc895f0e7cf62d82dfefccde6aeaca7c955e7120b635
Size	1.6 KB
Checksum	sha256:664784ecdc8c056cbd55fc895f0e7cf62d82dfefccde6aeaca7c955e7120b635
Downloads	1

Version	Date	Status	Downloads	Size
1.0.0	20 May 2026 15:30:11 (UTC)		1	1.6 KB