Single Cell RNA-Seq processing pipeline

This pipeline is designed to process single cell RNA-Seq data from raw reads to a count matrix. It uses nextflow pipeline.

This pipeline is developed for Oricchio Lab

Make sure to be added to docker group to run this pipeline. Contact the maintainers !!

Usage

Single Sell RNA-Seq pipeline

positional arguments:
  samplesheet           path to the samplesheet CSV file
  outdir                path to the output directory where to store the results

options:
  -h, --help            show this help message and exit
  --show                Print the command without running. Useful for testing. (default: False)
  -a ALIGNER, --aligner ALIGNER
                        aligner to use for alignment (default: cellranger)
  -g GENOME, --genome GENOME
                        genome to use for alignment (default: hg38)
  -p PROTOCOL, --protocol PROTOCOL
                        protocol used (default: 10XV3)

UPDATES (Date: 03 July 2025)

• Updated nf-core pipeline version to 4.0.0 (https://nf-co.re/scrnaseq/4.0.0/)
• The pipeline version can be over-written using the --version parameter.
• Added support to run pipeline with custom reference genomes (by providing a genome.fasta and annotations.gtf file)
• With the fasta + gtf option, the pipeline also by default saves the generates reference genome for later uses.
• CellBender call removed from pipeline, as it was taking too long to run. This can always be run separately if needed.

Sample sheet

Remember to have the first line "exactly" as sample,fastq_1,fastq_2

Problems ?

• java issues? Make sure to run pipeline can see the correct java installations. This could be happening if you are inside a virtual environment where a separate installation of java exists.

TODOs

• max cpu and max memory arguments unused

---

Maintained by - [divyanshu srivastava] (https://github.com/divyanshusrivastava)