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Nextflow Modules

Showing 2,273 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 quality control multiqc Collects QC statistics from CellBender 0.2 and 0.3 remove-background outputs into a summary TSV, a multi-page PDF (training curves, CellBender-style cell calling, latent PCA, soup fractions and per-gene removal) and MultiQC custom content.
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/cellbender/removebackground_v02 Process cellbender cellbender-0.2 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 0.2 (0.2.2), producing a per-sample output directory with filtered count matrices.
cellgeni/cellbender/removebackground_v03 Process cellbender cellbender-0.3 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 0.3 (0.3.2), 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/irods/loadcatalog Process irods download data transfer collection Downloads a whole iRODS collection with iget, keeping its folder layout and skipping files with unwanted extensions (e.g. BAM/CRAM/FASTQ).
cellgeni/multiqc Process multiqc qc report custom content Aggregates tool outputs and MultiQC custom content (*_mqc.* files) into a single HTML report, with a fixed output layout (multiqc_report.html and multiqc_data/) whatever the report title.
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