Nextflow Registry | nf-core/qcatch@0.0.0-0c7146d

nf-core/qcatch @ 0.0.0-0c7146d

Cell-filtering and QC reporting tool for alevin-fry quantification results

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @wzheng0520 @dongzehe

Maintainers: @wzheng0520 @dongzehe

Cell-filtering and QC reporting tool for alevin-fry quantification results

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

include { QCATCH } from 'nf-core/qcatch'

MIT License

Process

`Name`	`QCATCH`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`chemistry` string	Chemistry type for the single-cell experiment, which determines the partition range for the empty_drops step. Supported values: '10X_3p_v2', '10X_3p_v3', '10X_3p_v4', '10X_5p_v3', '10X_3p_LT', '10X_HT'. If using a standard 10X chemistry and quantification was performed with simpleaf (v0.19.5 or later), QCatch will try to infer the correct chemistry from the metadata.
`quant_dir` directory	Directory containing alevin-fry quantification results (af_quant output from simpleaf quant). Must contain the quantification matrix and associated metadata files.

Output 4 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.html` file	HTML QC report generated by QCatch containing visualizations and metrics `*.html`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 filtered_h5ad tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_filtered_quants.h5ad` file	Filtered quantification matrix in h5ad format (AnnData) `*_filtered_quants.h5ad`

#4 metrics_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_metrics_summary.csv` file	CSV file containing summary metrics from QC analysis `*_metrics_summary.csv`

Tool	Description	Homepage
qcatch	QCatch is a quality control and cell filtering tool designed for single-cell RNA-seq data processed by alevin-fry. It generates comprehensive QC reports and filtered count matrices.	https://github.com/COMBINE-lab/QCatch

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:29:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fqcatch/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/qcatch/blobs/sha256:a5c9ee955e33a979479d9a0a4cb0ea8d62f60356a3db19e9c4a61b0e23693ad1
Size	3.5 KB
Checksum	sha256:a5c9ee955e33a979479d9a0a4cb0ea8d62f60356a3db19e9c4a61b0e23693ad1
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:39:15 (UTC)		3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:29:41 (UTC)		2	3.5 KB