Add metabomics-lcms-preprocessing WF

[lecorguille]

Here is a first WF for metabolomics link to this GTN.

It would be great to have it in WorkflowHub.eu. We plan a paper which will refere to.

[mvdbeek]

Thanks @lecorguille, can you please have a look at the steps in https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

[lecorguille]

Thanks @lecorguille, can you please have a look at the steps in https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

Should be ok now?

[mvdbeek]

Yes, looks better but you're still missing the readme and changelog.

[lldelisle]

Also, could you rename the _test.yml to -tests.yml? Thanks

[mvdbeek]

Would it make sense to create a metabolomics folder under workflows/ ?
So your first workflow would then be in the workflows/metabolomics/lcms-preprocessing ?

[mvdbeek]

Does it make sense to provide a link to a template here (or link to the corresponding tutorial section) ?

[lecorguille]

As explained the line after, the template can be generated with the xcms get a sampleMetadata file tool.

The tool will fill the samplename based on the infile names.

[lecorguille]

Would it make sense to create a metabolomics folder under workflows/ ?
Done 👍

[lecorguille]

How can I generate a .workflowhub.yml?

[mvdbeek]

You don't have to, that's autogenerated

[lldelisle]

Could you rename the '-test.yml' to '-tests.yml' (the documentation is wrong, I just realized) and regenerate the .dockstore.yml, please? (planemo dockstore_init .)
For the moment, there is no test in the dockstore so the CI does not test.

[lecorguille]

Could you rename the '-test.yml' to '-tests.yml' (the documentation is wrong, I just realized)

Done

and regenerate the .dockstore.yml, please? (planemo dockstore_init .)

Already done, isn't it?

[lldelisle]

You need to regenerate it after having renamed your test, this way, it will add something like:

iwc/workflows/epigenetics/atacseq/.dockstore.yml

Lines 7 to 8 in 7fbbd2a

	testParameterFiles:
	- /atacseq-tests.yml

[lldelisle]

Apparently the renaming was sufficient to run the CI but it is better is you tell dockstore that you have a test file.

[lecorguille]

Oups, sorry, I missed the re in regenerate

[lldelisle]

No problem.

[mvdbeek]

Looks great from my side, what do you think @lldelisle ?

[lldelisle]

After this small correction in the README, it is good for me also.

[lldelisle]

Youhou! I am super happy to have new workflows in IWC.