NFDI4Ing Scientific Workflow Requirements

[Philipp Diercks]

Dear developers of Nextflow!

in a project within the German National Research Data Infrastructure (NFDI) initiative (for the engineering sciences, https://nfdi4ing.de/de), we are currently developing a portfolio of tools for the creation and documentation of reproducible simulation workflows.
For this purpose, we have created a repository (https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements), including an online documentation, to discuss how scientific workflows should be created/packaged/published in order to be as FAIR as possible.
We want to evaluate if existing workflow management systems provide the required features we have identified for our community, the engineering sciences.

So far, as source of information we have used the online documentation available for Nextflow, and implemented a "simple use case" representative of workflows in the engineering sciences to learn about Nextflow.
We hope for your contributions in correcting any misconceptions or misinterpretation.

We kindly ask you to review
    (a) the example implementation of the simple use case,
    (b) a manuscript we prepared to explain the results of our evaluation
and look forward to your feedback.

The example implementation of the simple use case can be found here:
https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/tree/main/simple_use_case
The manuscript can be found here:
https://bambund-my.sharepoint.com/:b:/g/personal/philipp_diercks_bam_de/Eb71SIAtyyFEvHN6i2rBZMQBB1Y6nb1KyoTLyIIBakPzhw?e=uz0pZ0
For more information on the context within NFDI4Ing, we refer to the key challenges & objectives of the archetype BETTY:
https://nfdi4ing.de/archetypes/betty/

Best regards,
On behalf of the team,
Philipp Diercks

Bundesanstalt für Materialforschung und –prüfung (BAM)

M. Sc. Philipp Diercks
7.7 Modeling and Simulation

Unter den Eichen 87
12205 Berlin
GERMANY

Phone: + 49 30 8104-4037
E-mail: philipp...@bam.de

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[Paolo Di Tommaso]

Hi Philipp, 

Thanks for including Nextflow in your workflow systems assessment initiative. 

The pipeline code looks well written. Maybe it can be strengthened in some areas. I'll submit a pull request in your repository at my earliest convenience. 

I've tried to execute the code and the step `makePoltOverLine` failed with this error message 

```

  pvbatch: error while loading shared libraries: libEGL.so.1: cannot open shared object file: No such file or director

```

I guess something is failing in the dependencies resolution in my Linux box. In this regard, I'd strongly advise creating Docker containers starting from your Conda recipes. In our experience, it makes the execution much more reliable. 

Best,
Paolo

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[Philipp Diercks]

Hi Paolo!

thank you for your message. I am looking forward to that PR  :)

We encountered the same problem and included a step to install the missing libraries in our github actions pipeline.

You can find the action here: https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/.github/actions/install-basic-deps/action.yml

We will also consider building a docker image for the simple use case.

Best regards,

Philipp

To view this discussion on the web visit https://groups.google.com/d/msgid/nextflow/CADgKzdzpZ4rtn5VRZowKLpvae4QF%2BtpO4fco9%2B%3DN9iis-LcSog%40mail.gmail.com.