Nextflow Registry | nf-core/scanpy/filter@0.0.0-6c4ed3a

nf-core/scanpy/filter @ 0.0.0-6c4ed3a

Filter cells and genes in single-cell RNA-seq data using Scanpy

filter quality-control scanpy single-cell preprocessing

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @nictru

Maintainers: @nictru

Filter cells and genes in single-cell RNA-seq data using Scanpy

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

include { SCANPY_FILTER } from 'nf-core/scanpy/filter'

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 `var` of the AnnData object. Use `index` if the gene symbols are the row names.

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:43:32 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fscanpy%2Ffilter/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/scanpy/filter/blobs/sha256:560b4e443994f793fb997c32cc40d42b45b304a60e166b53de5c6432c5bffdfa
Size	3.5 KB
Checksum	sha256:560b4e443994f793fb997c32cc40d42b45b304a60e166b53de5c6432c5bffdfa
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:32 (UTC)		3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:34:22 (UTC)		3	3.5 KB