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Some workflow test updates #2045

Merged
merged 6 commits into from
Oct 3, 2020
Merged

Some workflow test updates #2045

merged 6 commits into from
Oct 3, 2020

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cat-bro
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@cat-bro cat-bro commented Oct 3, 2020

Tests added/updated for

topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga
topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga
topics/metagenomics/tutorials/general-tutorial/workflows/amplicon.ga
topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga

Test are copied and adapted from usegalaxy-eu/workflow-testing (discussed in usegalaxy-eu/workflow-testing#3)

@cat-bro cat-bro requested review from a team as code owners October 3, 2020 02:45
bgruening
bgruening reviewed Oct 3, 2020
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topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-job.yml Outdated
class: File
location: https://zenodo.org/record/815875/files/trainset16_022016.pds.fasta
trainset_taxonomy:
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/trainset16_022016.pds.fasta
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@cat-bro do you know which URL type is the recommended one? You changed it here to be a UID like. But below you are using https://zenodo.org/record/1051552/files/HEK_SILAC-K6R6_ST905_part.mzml the record ones again.

I'm wondering if one more stable than the other?

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@bgruening I don't know which URL is recommended. The files urls are used in the data libraries. There was probably no need to update the links in this case.

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Do you want to redo the changes to this file then? Otherwise 👍 from me! Thanks.

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done :--)

@bgruening
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ping @simonbray

simonbray
simonbray reviewed Oct 3, 2020
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topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md
@@ -89,7 +89,7 @@ A prepared file is available via Zenodo. Alternatively, you can prepare the file
> ### {% icon comment %} Alternative upload
> As an alternative option, if you prefer to upload the cleaned file directly from Zenodo, you can do so with the following link:
> ```
> https://zenodo.org/record/2598415
> https://zenodo.org/record/2598415/files/1AKI_clean.pdb
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Thanks 👍

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simonbray commented Oct 3, 2020 •
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The changes to the workflow files look good to me, thanks! I think I'm lacking a bit of context about why it's necessary to move the tests from the workflow-testing repo, but I'm sure it's fine.

simonbray
simonbray previously approved these changes Oct 3, 2020
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The changes to the workflow files look good to me, thanks! I think I'm lacking a bit of context about why it's necessary to move the tests from the workflow-testing repo, but I'm sure it's fine.

We do not want to duplicated workflows. See the discussion here: usegalaxy-eu/workflow-testing#3

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cat-bro commented Oct 3, 2020

@simonbray the workflow files in workflow-testing have fallen out of date with the workflows here, which are really the ones that we want to test. Having tests in this repo means that we can always be running them on current versions.

@bgruening bgruening merged commit 163ebcf into galaxyproject:master Oct 3, 2020
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Thanks!

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@bgruening bgruening bgruening approved these changes

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@cat-bro @bgruening @simonbray