Nextflow Registry | nf-core/metaspace/download@0.0.0-0c7146d

nf-core/metaspace/download @ 0.0.0-0c7146d

A module to download dataset results from the METASPACE platform and save them as CSV files, using a containerized Python script. Inputs are provided via a CSV file or a list of datasets, with results saved to a specified output directory.

metaspace metabolite annotation data-download csv

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Dewey-Wang

Maintainers: @Dewey-Wang

Summary

Get started

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

include { METASPACE_DOWNLOAD } from 'nf-core/metaspace/download'

License

MIT License

Process

`Name`	`METASPACE_DOWNLOAD`

Input 1 channel

#1 tuple

`dataset_id` string	The ID of the dataset to process. The ID is the last part of the dataset URL. For example, in the URL `https://metaspace2020.org/dataset/2022-08-05_17h28m56s`, the `dataset_id` is `2022-08-05_17h28m56s`.
`database` string	The database to download the dataset from (default: 'HMDB'). If not provided, all dataset will be included.
`version` string	The version of the database to download the dataset from (default: 'v4'). If not provided, all versions will be included.

Output 3 channels

#1 log

`emit:` string	The standard output (stdout) of the script, containing log messages. You can print the last log to see the download progress of all the datasets. Example: METASPACE_DOWNLOAD.out.log.view { "${it.split('\n').last().trim()}" } It will print the last log message of the script. For Example: "❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset." "❌ {dataset_id} could not find database: {database}" "❌ {dataset_id} has no annotation data in database: {database}." "⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}" "✅ {dataset_id} with {database} database are saved to {filename}" "✅ {dataset_id} with all database are saved to {filename}"

emit: string

The standard output (stdout) of the script, containing log messages. You can print the last log to see the download progress of all the datasets. Example: METASPACE_DOWNLOAD.out.log.view { "${it.split('\n').last().trim()}" } It will print the last log message of the script. For Example: "❌ {dataset_id} Dataset not found or inaccessible. Skipping this dataset." "❌ {dataset_id} could not find database: {database}" "❌ {dataset_id} has no annotation data in database: {database}." "⚠️ {dataset_id} has multiple {database} version. All the version saved to {filename}" "✅ {dataset_id} with {database} database are saved to {filename}" "✅ {dataset_id} with all database are saved to {filename}"

#2 results

`${dataset_id}_*.csv` file	CSV file containing the downloaded dataset results, saved to the directory specified by the output parameter. Filename format is '{dataset_id}_.csv'. `.csv`

#3 versions

`versions.yml` file	YAML file containing the versions of the tools used in the pipeline. This file is automatically generated by the pipeline and should not be modified. `versions.yml`

Tool	Description	Homepage
metaspace2020	Python package providing programmatic access to the METASPACE platform	https://metaspace2020.readthedocs.io

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:55:29 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmetaspace%2Fdownload/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/metaspace/download/blobs/sha256:c6699afa4553f78916617daa09e26844e137790e2efbad7441cfd8c0daa4af21
Size	5.2 KB
Checksum	sha256:c6699afa4553f78916617daa09e26844e137790e2efbad7441cfd8c0daa4af21
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:55:29 (UTC)		1	5.2 KB	-