Nextflow Modules
Showing module(s) with keyword "10x"
| Module | Keywords | Description |
|---|---|---|
| cellgeni/cellranger/count | 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 | 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/rename10xsample | 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/sra2fastq | 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 | 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 | 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. |
| nf-core/bamtofastq10x | bam convert fastq 10x | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis |