nf-core/metaspace/converter @ 0.0.0-0c7146d
Summary
Export METASPACE datasets to AnnData and SpatialData objects
Get started
Add the following snippet to your workflow script to include this module.
include { METASPACE_CONVERTER } from 'nf-core/metaspace/converter'
License
MIT License
Process
Name
|
METASPACE_CONVERTER |
|---|
Input
6 channels
ds_id
string
|
METASPACE dataset identifier to retrieve and convert to AnnData and SpatialData formats. |
|---|
database_name_
string
|
Name of the metabolite annotation database to use (e.g., HMDB) |
|---|
database_version_
string
|
Version of the annotation database to use (e.g., v4) |
|---|
fdr_
string
|
False Discovery Rate threshold for filtering metabolite annotations. ^(0(\.[0-9]+)?|1(\.0+)?)$
|
|---|
use_tic_
string
|
Controls whether intensity values are scaled by the total ion count per pixel. ^(true|false)$
|
|---|
metadata_as_obs_
string
|
Whether to store metadata in the obs dataframe instead of uns. ^(true|false)$
|
|---|
Output
3 channels
#1
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
#2
adata_object
AnnData_${ds_id}.h5ad
file
|
AnnData object in .h5ad format. Obs are single pixels and vars are metabolites |
|---|
#3
sdata_object
SpatialData_${ds_id}.zarr
directory
|
SpatialData format in .zarr format |
|---|
| Tool | Description | Homepage |
|---|---|---|
| metaspace_converter | Python package to download and convert datasets from the METASPACE knowledge base to common formats for single-cell and spatial omics analysis | https://metaspace2020.github.io/metaspace-converter/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:55:27 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmetaspace%2Fconverter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/metaspace/converter/blobs/sha256:a1f50a6b4803333809d4209defd2e9c76d0ba22fc233d5d5a27a7c2b88fdf266 |
| Size | 3.8 KB |
| Checksum | sha256:a1f50a6b4803333809d4209defd2e9c76d0ba22fc233d5d5a27a7c2b88fdf266 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:55:27 (UTC) | 1 | 3.8 KB | - |