chore: remove wrapper for unmaintained nanosim-h in favor of new nanosim wrapper (#3165)
#3143
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WalkthroughThe changes involve enhancements to the Changes
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Files selected for processing (3)
- bio/nanosim-h/meta.yaml (1 hunks)
- bio/nanosim-h/test/Snakefile (1 hunks)
- bio/nanosim-h/wrapper.py (2 hunks)
Additional context used
Path-based instructions (1)
bio/nanosim-h/wrapper.py (2)
Pattern
**/*.py: Do not try to improve formatting.
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**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
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Additional comments not posted (11)
bio/nanosim-h/test/Snakefile (4)
3-3: LGTM!The explicit definition of the
fastaparameter improves clarity and usability.
6-8: LGTM!The reformatting of the
outputsection improves consistency.
10-14: LGTM!The expanded
paramssection enhances functionality and flexibility by allowing users to specify a broader range of parameters.
16-16: LGTM!The update to the
logsection improves consistency with the new formatting style.bio/nanosim-h/meta.yaml (3)
2-5: LGTM!The reformatting of the
descriptionto block style improves readability.
8-8: LGTM!The addition of the
urlfield enhances accessibility by providing a reference point for users.
10-24: LGTM!The expanded
paramssection with detailed descriptions improves the documentation quality, making it easier for users to understand how to configure the simulator effectively.bio/nanosim-h/wrapper.py (4)
32-39: LGTM!The additional parameters enhance the function's capability to manage input data more effectively.
Tools
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32-39: LGTM!The updates to the
prefixparameter and the introduction ofinput_fastaandinput_profile_dirimprove the flexibility and usability of the function.Tools
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60-60: LGTM!The update to the command string ensures that the new input parameters are passed correctly in the command execution.
32-39: Skip the static analysis hints.The use of
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Just wondering what the advantage would be of having all parameters separately (instead of a single |
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Yeah, I also saw that. Also, it might make sense to run stuff in a temporary directory and then copy to truly arbitrary file path and names. But I think I think it is not worth investing too much in this wrapper, as So for my own usage, I am now working on a wrapper for the original tool, |
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Just fixed the formatting, so I hope all tests will run through, now. Feel free to review and merge, if you are satisfied, @fgvieira. Also, the newer |
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Hmm, I can't seem to get Should we maybe remove this old wrapper altogether? It will still exist in the older |
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Yep, if we cannot get it to work and @johanneskoester has nothing against it, I agree that it is better to just remove it. |
dlaehnemann
changed the title
nanosim-h input file handlingnanosim-h in favor of new nanosim wrapper (#3165)
fgvieira
deleted the
feat/more-specific-nanosim-h-input-file-handling
branch
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
max_read_lenparameter to thenanosimhrule, allowing for longer simulated reads.Improvements
Bug Fixes