RNA-Seq Pipeline Test Version

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

Minimum Requirements

To run the pipeline, you will need the following:

1. Sample Sheet: A sample sheet that contains the necessary information about your sequencing samples. Here is an example of a sample sheet for a single paired-end sample:

   id,r1,r2
   test,test_1.fastq.gz,test_2.fastq.gz
   

2. Reference Genome: The genome sequence in FASTA format.
3. Gene Annotation File: A gene annotation file in GTF format.

Running the Pipeline

Once you have the required files, you can run the pipeline with the following command:

nextflow run tyfu-cc/rnaseq \
    --input /path/to/sampleshee.csv \
    --outdir /path/to/where/the/outputs/are/stored \
    --fasta /path/to/genome.fa \
    --gtf /path/to/genes.gtf

Detailed Usage

See detailed usage here.