nf-core/scanpy/pca @ 0.0.0-6c4ed3a
Summary
Perform principal component analysis (PCA) on single-cell RNA-seq data using Scanpy
Get started
Add the following snippet to your workflow script to include this module.
include { SCANPY_PCA } from 'nf-core/scanpy/pca'
License
MIT License
Process
Name
|
SCANPY_PCA |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
h5ad
file
|
AnnData object in h5ad format *.{h5ad}
|
key_added
string
|
Key to add to obsm with PCA coordinates, usually 'X_pca' |
|---|
Output
3 channels
#1
h5ad
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.h5ad
file
|
AnnData object with PCA coordinates added *.h5ad
|
#2
obsm
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
X_*.pkl
file
|
Pickle file containing PCA coordinates matrix X_*.pkl
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| scanpy | Single-Cell Analysis in Python | https://scanpy.readthedocs.io |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:43:35 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fscanpy%2Fpca/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/scanpy/pca/blobs/sha256:9b82adb7e276cb6c144ad80a71dad8df161fd6ed0808510a3b7c2d28952f5a7e |
| Size | 3.2 KB |
| Checksum | sha256:9b82adb7e276cb6c144ad80a71dad8df161fd6ed0808510a3b7c2d28952f5a7e |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:43:35 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:34:26 (UTC) | 3 | 3.2 KB |