Running The pipeline with the test data

Test data contains 20 open-access pair-end RNAseq samples from GEUVADIS study.

To execute the pipeline with reference and annotation files they should be manually downloaded first:

# Make sure you are in the root directory of the pipeline (where the main.nf is located)
wget ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/references/rnaseq_complete_reference_290322.tar.gz
tar -xzvf rnaseq_complete_reference_290322.tar.gz
rm rnaseq_complete_reference_290322.tar.gz

After these steps you should have rnaseq_complete_reference folder in the pipeline directory.

Then you can start the pipeline using test profile

nextflow run main.nf -profile test

If you have a specific needs for your local cluster please prepare the configuration file accordingly. As example you cna check-out configuration file prepared for University of Tartu HPC

Users of University of Tartu HPC can run the pipeline with test dataset using the pre-generated sbatch script:

sbatch run_GEUVADIS_test.sh