nf-core/scanpy/filter @ 0.0.0-0c7146d
Summary
Filter cells and genes in single-cell RNA-seq data using Scanpy
Get started
Add the following snippet to your workflow script to include this module.
include { SCANPY_FILTER } from 'nf-core/scanpy/filter'
License
MIT License
Process
Name
|
SCANPY_FILTER |
|---|
Input
7 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
h5ad
file
|
AnnData object in h5ad format *.{h5ad}
|
#2
tuple
min_genes
integer
|
Minimum number of genes expressed per cell |
|---|
#3
tuple
min_cells
integer
|
Minimum number of cells expressing each gene |
|---|
#4
tuple
min_counts_gene
integer
|
Minimum number of counts per gene |
|---|
#5
tuple
min_counts_cell
integer
|
Minimum number of counts per cell |
|---|
#6
tuple
max_mito_percentage
integer
|
Maximum percentage of mitochondrial genes per cell |
|---|
#7
tuple
symbol_col
string
|
Column name of the gene symbols in the |
|---|
Output
2 channels
#1
h5ad
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.h5ad
file
|
Filtered AnnData object *.h5ad
|
#2
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 19:10:44 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fscanpy%2Ffilter/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/scanpy/filter/blobs/sha256:3941df517c408ee3518cdb9b888045c64ac72ab05423841788cf3d15f9bf8520 |
| Size | 3.5 KB |
| Checksum | sha256:3941df517c408ee3518cdb9b888045c64ac72ab05423841788cf3d15f9bf8520 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:44 (UTC) | 1 | 3.5 KB | - |