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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)

Genomes available

  1. Human -
    • GRCh37
    • GRCh38
    • hg19
    • hg38
  2. Mouse -
    • GRCm38
    • mm10

Defaults

The pipeline uses the following default nextflow parameters.

VERSION = '2.7.0'
MAX_MEMORY="100.GB"
MAX_CPUS=12

Sample sheet

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

NOTE

This pipeline runs cellranger: 8.0.0.

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