Add docstrings to nextflow functions, modules, and workflows #62
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bergsalex
reviewed
Aug 26, 2025
| fi | ||
| else | ||
| echo "\${file} exists, adding to process list." | ||
| echo "\${file}" >> files_to_process.txt |
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Is there a missing fi after this else block?
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And also does the while loop need to be closed with a done ?
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Both should be there, but github might be hiding your context.
This patch should have been separate, but it fixes behavior when you want to ignore invalid inputs -- it used to place the file in the list to process and would just crash later.
nextflow/modules/jabs_classifiers.nf
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| * @param tuple | ||
| * - in_pose The input pose file. | ||
| * - feature_cache The directory containing the generated features. | ||
| * @param classifiers A map of classifier names to their respective parameters. |
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You document the tuples, it might be nice to document what the map looks like.
e.g.
@param classifiers A map where each entry contains:
- key: classifier name (string)
- value: object 🤷
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How about:
* @param classifiers A map of classifiers:
* - classifier_name: a list of classifier parameter maps:
* - stitch_value: the gap size for stitching behavior bouts
* - filter_value: the minimum length for behavior bouts
I think the nested maps might get a bit verbose...
C-1337ka
approved these changes
Sep 17, 2025
gbeane
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Sep 17, 2025
SkepticRaven
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YODA-193-add-docstrings-to-nextflow-functions-modules-and-workflows
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My attempt to meld javadoc style/intent into nextflow documentation.
Changes from javadoc:
@publishtag to indicate when a workflow or process publishes data outside its workdir.@returntag, since nextflow is MIMO.Features that might be useful in docstrings but not added:
param.*) used in processes/workflows not listed. javadoc has a@notetag, which could be used for noteworthy parameters.