...

You will require a basic knowledge of Linux/Unix commands to be able to participate effectively in this workshop. If you don’t, please attend the following training [Introduction to HPC].

7. Nextflow pipeline outputs and PBS outputs

Results folder

The results are output in the folder name specified in the .nexftlow.config file under the outdir parameter. It is generally set to be results.

// nextflow.config
params {
  outdir = 'results'
}

Nextflow log, metrics and reports

By default, Nextflow will create a log file in the working directory called .nextflow.log. This file is hidden but you can see it using the command:

ls -a

If you rerun the pipeline in the same folder, the previous .nextflow.log will be renamed .nextflow.log.1 and a new .nextflow.log will be generated.

You can change the default location by specifying a different location

nextflow -log ~/code/nextflow.log run  

PBS output

8. Where to from now?

Nextflow offers free Fundamentals Training: https://training.nextflow.io/basic_training/

Provide links to carpentry course: https://carpentries-incubator.github.io/workflows-nextflow/instructor/01-getting-started-with-nextflow.html