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Nextflow Modules

Showing 2,230 module(s)

Module Kind Keywords Description
cellgeni/anndata/concat Process concatenation single-cell anndata In-memory concatenation of AnnData objects using anndata.concat.
cellgeni/anndata/concatondisk Process concatenation single-cell anndata Memory-efficient on-disk concatenation of AnnData objects using anndata.experimental.concat_on_disk.
cellgeni/cellbender/qc Process cellbender single-cell RNA-seq quality control ambient RNA Collects summary statistics from CellBender outputs and produces a QC report directory with PDF plots and per-sample RDS summaries.
cellgeni/cellbender/removebackground Process cellbender single-cell RNA-seq ambient RNA empty droplets artifact removal Removes ambient RNA and empty droplet artifacts from single-cell RNA-seq data using CellBender, producing a per-sample output directory with filtered count matrices.
cellgeni/cellranger/count Process cellranger 10x single-cell RNA-seq count matrix Runs Cell Ranger count on 10x single-cell RNA-seq FASTQs to align reads, generate feature-barcode matrices, and produce per-sample output directories.
cellgeni/fetch10xmeta Process metadata GEO SRA ENA ArrayExpress BioProject 10x single-cell public data Fetches and parses metadata for public 10x datasets from GEO (GSE*), ArrayExpress (E-MTAB*), or BioProject (PRJ*). Downloads raw metadata from SRA/ENA/BioStudies, resolves sample-to-run mappings, classifies each run by download type, and produces a merged links file.
cellgeni/hmetacells Process metacells hierarchical-clustering single-cell scRNA-seq scATAC-seq Hierarchical metacell aggregation for single-cell genomics data.
cellgeni/irods/getfile Process iRODS download checksum md5 Downloads a file from iRODS to the local working directory and verifies its integrity by comparing the local MD5 checksum against the iRODS-recorded checksum.
cellgeni/irods/getmetadata Process irods metadata csv Module to get metadata from an iRODS collections and data objects and output as CSV
cellgeni/irods/listcollection Process iRODS data management collection List the contents of an iRODS collection and write results to a CSV file.
cellgeni/rename10xsample Process 10x single-cell FASTQ rename Cell Ranger sample Collects per-run Cell Ranger-style FASTQs for a sample and renames them to a consistent sample-level naming scheme, ready for downstream alignment.
cellgeni/scanpy/aggregate Process pseudobulk aggregation single-cell scRNA-seq scanpy Pseudobulk aggregation of an AnnData object using scanpy.get.aggregate.
cellgeni/seacells Process metacells single-cell scRNA-seq scATAC-seq aggregation SEACells aggregates single-cell profiles into metacells from scRNA-seq or scATAC-seq data.
cellgeni/sra2fastq Process SRA FASTQ conversion single-cell 10x public data Converts a local SRA file to split gzipped FASTQ files using parallel-fastq-dump, producing one FASTQ per read slot ready for downstream processing.
cellgeni/starsolo10x Process STARsolo STAR alignment single-cell 10x RNA-seq count matrix Aligns 10x single-cell RNA-seq FASTQs to a reference genome using STARsolo, producing per-sample output directories with count matrices and summary statistics.
cellgeni/starsoloqc Process STARsolo STAR QC quality control single-cell 10x RNA-seq Collects QC statistics from STARsolo output directories, producing a merged TSV summary of alignment and cell-calling metrics across all samples in a dataset.