FIRST_RUN.md

Try the workflow

This small tutorial will explain to you how to run CAW on a small sample test data. Some variables are specific to Swedish UPPMAX cluster, but can be easily modified to suit any clusters.

Make a test directory

mkdir test_CAW
cd test_CAW

Test the workflow on a test tiny set

This workflow itself needs no installation. Nextflow will automatically fetch it from GitHub when launched if SciLifeLab/CAW is specified as the workflow name.

nextflow run SciLifeLab/CAW --test

If you're using a Swedish UPPMAX cluster, don't forget to provide your project ID.

nextflow run SciLifeLab/CAW --test --project <UPPMAX Project ID>

Other possibility for advanced users

Clone the repository and test the workflow on a test tiny set

You can download the repository yourself from GitHub and run them directly:

git clone https://github.com/SciLifeLab/CAW test_CAW
cd test_CAW
nextflow run main.nf --test

Load Nextflow

If you're running on a Swedish UPPMAX cluster you can load Nextflow as an environment module:

module load Nextflow

Environnement variables are set up each time the module is loaded, so you might want to set them up after loading the module.

Running tests in interactive mode on milou

You can try the test data by changing to the interactive mode on milou and run the test tiny set like:

$ interactive -A <UPPMAX Project ID> -p node
[ ... login messages ... ]
$ nextflow run main.nf -profile interactive --test --project <UPPMAX Project ID>

For more tests, see Usage documentation