RNAseq pipeline

Usage

First, prepare a sample datasheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
sample1,<path/to/fastq_1_file>,<path/to/fastq_2_file>
sample2,<path/to/fastq_1_file>,<path/to/fastq_2_file>

Now, you can run the pipeline using:

nextflow run ./workflows/main.nf \
  --input <path/to/input_samplesheet> \
  --genomeFasta <path/to/input_genomeFasta> \
  --gtfFile <path/to/gtfFile> \
  [--amd/--arm] \
  -entry RNASEQ

Important

The pipeline can be run with either --amd or --arm, depending on the architecture of the user's operating system. If nothing is specified, the pipeline is run using --amd by default.

Note

To run the pipeline on the test data, you need to download the gtf and genome files and unzip them.