nf-core/scanpy/pca @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:10:47 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fscanpy%2Fpca/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/scanpy/pca/blobs/sha256:cd6dbc8680b4642229a89b91778902eebd9497db19cebc21b545d2712adf9637 |
| Size | 3.2 KB |
| Checksum | sha256:cd6dbc8680b4642229a89b91778902eebd9497db19cebc21b545d2712adf9637 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:47 (UTC) | 1 | 3.2 KB | - |