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📝 WalkthroughWalkthroughAdds documentation: a new "Workflow profiles" / "The 'profiles' Directory" section and table-of-contents entry in Changes
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README.md(1 hunks)profiles/README.txt(1 hunks)
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🪛 LanguageTool
profiles/README.txt
[style] ~8-~8: Consider using a less common alternative to make your writing sound more unique and professional.
Context: ... pitfalls or other things to consider. Feel free to open pull requests for 3rd party workfl...
(FEEL_FREE_TO_STYLE_ME)
[grammar] ~9-~9: Use a hyphen to join words.
Context: ... Feel free to open pull requests for 3rd party workflows you are working with to ...
(QB_NEW_EN_HYPHEN)
[grammar] ~9-~9: Ensure spelling is correct
Context: ...n during development, e.g. plotting and dowload rules.
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
README.md
[grammar] ~59-~59: Ensure spelling is correct
Context: ...cular execution environment (cluster or cload). You may include a readme file next to...
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
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README.md (1)
10-15: Add the new section to the table of contents.The "The 'profiles' Directory" section should be added to the table of contents for consistency and to help users navigate the documentation.
Apply this diff to update the table of contents:
- [Snakemake workflow: `<name>`](#snakemake-workflow-name) - [Usage](#usage) - [Deployment options](#deployment-options) + - [The 'profiles' Directory](#the-profiles-directory) - [Authors](#authors) - [References](#references) - [TODO](#todo)
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- profiles/README.txt
🔇 Additional comments (1)
README.md (1)
53-59: Good typo fix and clear documentation.The spelling error flagged in the previous review ("cload" → "cloud") has been corrected, and the new section provides clear guidance on the profiles directory structure and purpose.
m-jahn
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m-jahn
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Hi Christian, great idea to include profiles!
I have some general comments that could be addressed to make this even more user-friendly:
- maybe change the README.txt to a README.md in line with all other markdown docs we use for documentation? This would also include the file in automatic md linting by Github actions
- would you like to include an actual dummy profile? Or would that conflict with other parts of a workflow template? From my point of view that would be OK since profile will stay silent until it is invoked with
snakemake --profileright? If we like to encourage the use of profiles, a real working profile including a statement how to invoke it would be a really cool addition.
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@m-jahn will switch to lower case and add a template for this particular workflow. Will only able to do this by the end of the week. |
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thanks for doing this! |
dlaehnemann
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dlaehnemann
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I also think this is a great idea, and just double-checked that the profiles/ directory also gets copied by snakedeploy.
The code does it, but I had to add a PR that adds the profiles/ directory copy info to the snakedeploy docs.
And here, I just edited the text heavily and removed redundancy by making the text in the main README.md really short and pointing to the profiles/README.md for details.
Also I:
- added in a bunch of linkouts to the relevant documentation pages
- differentiate between the
default/and other profiles - differentiate between generic and cluster-specific profiles
- mention that resource specification should go directly into rules, wherever a generic (dynamic) resource specification is feasible
In general, I kept all the info that was there. The only thing I removed was this sentence:
It may also be necessary to occasionally label certain rules of a particular workflow with the
localrules: <rule 1>, <rule 2>, ...directive when workflow developers focused on server execution during development, e.g., plotting and download rules.
It feels like something that should rather go into the snakemake profiles documentation somewhere, as this is a useful strategy for using profiles during development in general, right? @cmeesters, would you like to prepare a respective docs PR on snakemake?
Thanks for all your work, @dlaehnemann ! (I'm afraid, I cannot continue full throttle.) Do you mean some kind of outlink from the Snakemake docs or some entirely new paragraph there? Perhaps, it is time to start gathering to-do items for the hackathon, too ... |
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Hi David, can you commit those suggested changes if Christian doesn't have time (I understood it that way...@cmeesters)? |
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OK, I committed all of those suggestions and created an issue on the new (currently still private) project board for this year's hackathon. |
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Actionable comments posted: 2
🤖 Fix all issues with AI agents
In `@profiles/README.txt`:
- Line 1: Update the documentation phrase "workflow specific profile" to use a
hyphenated adjective: change it to "workflow-specific profile" in the README
text so the sentence reads "...a `config.yaml` file with a workflow-specific
profile". Locate the exact string "workflow specific profile" in the profiles/
README line and replace it with the hyphenated form to fix the grammar.
In `@README.md`:
- Around line 56-57: Update the README text to hyphenate "workflow-specific" and
fix the broken link by pointing to the new file name (profiles/README.txt)
instead of profiles/README.md; edit the sentence that mentions
"profiles/README.md" so it reads "The [profiles README](profiles/README.txt)
provides more details" (or similar) and ensure "workflow-specific profiles" is
hyphenated where it appears.
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3 participants
Snakemake workflows to be executed on cluster or cloud environments deployed with
snakedeploymeanwhile copy aprofilesdirectory, if present.This PR attempts to add an empty
profilesdirectory. It includes a brief description in theREADME.mdand adds a similar file in the profiles directory.Summary by CodeRabbit
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