Nextflow specific outputs

1 Nextflow report

Here, we described the following command to run the Nextflow pipeline locally:

nextflow run GPMelt_workflow.nf -c nextflow.config  -c nextflow_local.config -c user_params.config  -with-report reports/GPMelt_workflow_report.html 

The command -with-report reports/GPMelt_workflow_report.html will create a Nextflow report in the folder reports, together with the CO₂ footprint reports (see the nextflow.config file described in here, section 2)

We refer the user to the Nextflow tutorial to better understand the content of this report.

This report should be used to improve the resource requirement defined in the user_params.config file (see here, section 3).

Optimally, for each new dataset, you would first run the pipeline on few IDs with different properties (different number of conditions and replicates if possible) to have an idea of the average and maximal resource requirements of the pipeline for this dataset. Updating the user_params.config file accordingly, you would then run the pipeline on the full dataset.

2 CO₂ footprint report

We encourage you to have a look at the CO₂ footprint report generated by the nf-co2footprint plugin, also saved in the folder reports.

The current implementation is maybe non-optimal, but tuning the resource requirements can already help reducing our CO₂ footprint when running the pipeline!

Note: Interested in helping me making this more efficient? Contact me, I would be delighted to get help!!

Note: While report.overwrite is set to true in the nextflow.config file, the CO₂ footprint report does not always get overwritten. If you get an error message saying WARN: Failed to render CO2e footprint report -- see the log file for details, this might be solved by removing the current reports in the reports folder.