fix: python #158
fix: python #158
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WalkthroughThis pull request introduces modifications to the bioinformatics workflow and dependency management within the project. Key changes include the restructuring of the Changes
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This PR takes over from #157 regarding the replacement of tutorial and solution tasks. Also: it introduced the run directive more thoroughly. |
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@lukashellmann & @mptrsen if anyone of you could please review the - hopefully - improved slide sets. I intend to close this little series with a group job example and well-tested exercises in 2–3 days. |
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Actionable comments posted: 16
🧹 Outside diff range and nitpick comments (3)
setup_creators/environment.yaml (2)
21-21: LGTM! Consider specifying a version for seaborn.The addition of seaborn, a powerful statistical data visualization library, is a good choice for a bioinformatics project. It will enhance the data visualization capabilities of the workflow.
To ensure reproducibility and avoid potential compatibility issues in the future, consider specifying a version for seaborn. For example:
- seaborn =0.12.2 # or whatever version is appropriate for your project
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1-21: Overall, these changes improve dependency management.The modifications to this
environment.yamlfile enhance the project's dependency management in several ways:
- Using pip for pysam installation addresses version compatibility issues.
- The addition of seaborn expands data visualization capabilities.
- The restructuring of dependencies provides more flexibility.
To further improve:
- Consolidate the bcftools entries as suggested earlier.
- Consider adding version specifications for newly added or modified dependencies to ensure reproducibility.
These changes will contribute to a more robust and maintainable bioinformatics workflow.
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setup_creators/tutorial/06_Snakefile_run (1)
85-92: Consider placingsamtools_indexrule beforebcftools_callfor logical flowWhile Snakemake resolves dependencies irrespective of rule order, organizing your rules so that upstream dependencies are defined before their dependents can enhance the readability of your workflow. Placing
samtools_indexbeforebcftools_callclearly shows the flow from BAM sorting to indexing and then variant calling.
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setup_creators/environment.yaml
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🔇 Additional comments (6)
setup_creators/environment.yaml (1)
14-15: LGTM! The addition of pysam via pip is well-justified.The inclusion of pysam under a pip section is a good solution to the version compatibility issue with snakemake. This approach allows for more flexible dependency management.
Regarding the yamllint warning about indentation: The current indentation is correct for YAML structure. The warning appears to be a false positive, so no changes are needed.
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setup_creators/solutions/06_Snakefile_run (5)
4-8: Theallrule is correctly structuredThe
allrule correctly specifies the final outputs of the workflow, ensuring that Snakemake knows the desired end products.
9-17:bwa_maprule is properly definedThe
bwa_maprule accurately specifies the inputs and outputs, and the shell command correctly callsbwa memwith the appropriate inputs. The use of{input}and{output}is appropriate and should work as expected.
19-27:samtools_sortrule is correctly specifiedThe
samtools_sortrule correctly defines the inputs, outputs, and the shell command. The usage of{wildcards.sample}in the temporary file prefix with the-Toption is appropriate and helps in avoiding file name collisions during parallel execution.
29-36:samtools_indexrule is correctly implementedThe
samtools_indexrule properly indexes the sorted BAM files usingsamtools index, and the inputs and outputs are correctly specified.
38-48:bcftools_callrule is properly configuredThe
bcftools_callrule effectively usesbcftools mpileupandbcftools callto generate the VCF file. The use ofexpandto handle multiple samples for the BAM and BAI files is appropriate and ensures all samples are included in the variant calling.
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (9)
setup_creators/environment.yaml (2)
20-20: Consider adding a version constraint for seaborn.The addition of seaborn as a dependency is noted. However, to ensure consistency across different environments and for better reproducibility, it's recommended to specify a version constraint.
For example:
- seaborn >=0.11.0This ensures a minimum version while allowing for compatible updates.
11-20: Overall improvements in dependency management.The changes in this file significantly enhance the project's dependency management:
- The bcftools version constraint has been updated to be more flexible while maintaining a minimum version.
- The pysam installation method has been changed to use pip, addressing potential conflicts with snakemake. This change is well-documented with clear comments.
- Seaborn has been added as a new dependency, expanding the project's data visualization capabilities.
These modifications align well with the PR objectives of refactoring and improving the project structure. They also address the previous review comments effectively.
To further improve the file:
- Consider adding version constraints to other dependencies that don't have them (e.g., pygments, seaborn) for better reproducibility.
- Ensure that the addition of seaborn is reflected in the project documentation or README, if applicable.
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setup_creators/solutions/08_Snakefile_script2 (4)
7-9: Approve output reorganization with suggestionThe changes to the 'all' rule appropriately reflect the new output structure of the workflow. The addition of "calls/positions.png" and the relocation of "quals.svg" to the "calls/" directory improve organization.
Consider using a variable for the output directory to make future changes easier:
OUTPUT_DIR = "calls" rule all: input: f"{OUTPUT_DIR}/all.vcf", f"{OUTPUT_DIR}/positions.png", f"{OUTPUT_DIR}/quals.svg"This would allow easy modification of the output directory in the future.
43-44: Approve use of SAMPLES variable with suggestion for clarityThe changes in the 'bcftools_call' rule correctly utilize the new SAMPLES variable, ensuring all samples are processed. The use of expand() is appropriate for generating file paths.
To improve clarity, consider adding a comment explaining the expand() function:
input: fa="data/genome.fa", # Generate a list of BAM files for all samples bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES), # Generate a list of BAI files for all samples bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)This would help readers understand the purpose of the expand() function.
51-57: Approve new 'plot_positions' rule with suggestion for error handlingThe addition of the 'plot_positions' rule enhances the workflow by including a visualization step. The rule is correctly structured and uses the appropriate input and output.
Consider adding error handling to make the workflow more robust:
rule plot_positions: input: rules.bcftools_call.output output: "calls/positions.png" script: "scripts/plot-positions.py" log: "logs/plot_positions.log" conda: "envs/plotting.yaml" # Ensure this environment file existsThis addition would capture any errors in a log file and specify a conda environment for reproducibility.
61-65: Approve 'plot_quals' rule changes with suggestion for consistencyThe changes to the 'plot_quals' rule correctly align with the new output organization. The input and output paths are now consistent with other rules in the workflow.
For consistency with the 'plot_positions' rule, consider adding similar error handling and environment specification:
rule plot_quals: input: "calls/all.vcf" output: "calls/quals.svg" script: "scripts/plot-quals.py" log: "logs/plot_quals.log" conda: "envs/plotting.yaml" # Ensure this environment file existsThis would make both plotting rules consistent in terms of error handling and environment specification.
slides/creators/Python_in_Snakemake.tex (3)
55-55: Good addition of Snakemake API introductionThe new content introducing Snakemake's API and providing examples of
expand()andglob_wildcards()functions is a valuable addition. It gives users practical examples to work with and understand these important functions.Consider adding a brief explanation of why these functions are particularly useful in Snakemake workflows to provide more context for learners.
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200-289: Excellent introduction to thescriptdirectiveThe new section on "Snakemake's features for external Scripts" is a valuable addition to the course material. It clearly explains the
scriptdirective and provides examples in both Python and R, which is beneficial for users of both languages.Consider adding a brief comparison between the
runaction and thescriptdirective, highlighting when to use each approach. This could help learners understand the best practices for incorporating Python code in their Snakemake workflows.
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1-506: Overall excellent improvements to the Python in Snakemake course materialThe changes made to this file have significantly enhanced the educational content on using Python in Snakemake workflows. The additions and modifications provide a more comprehensive and practical guide for learners.
Key improvements include:
- Enhanced objectives with clearer learning goals
- New sections on the
runaction andscriptdirective- Practical examples and hands-on tasks for refactoring and debugging
- Improved explanations of Snakemake functions and API
- Updated debugging instructions for both Python and R scripts
To further polish the material:
- Double-check for any remaining typos or formatting inconsistencies.
- Consider adding a brief summary or recap section at the end to reinforce the key concepts covered.
- Ensure all code examples are consistently formatted and indented for optimal readability.
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slides/creators/Python_in_Snakemake.tex (4)
Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-07T18:50:01.657Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-07T18:49:29.039Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-07T18:50:30.670Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-07T18:48:51.479Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.
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setup_creators/environment.yaml
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🔇 Additional comments (5)
setup_creators/environment.yaml (2)
11-11: LGTM: bcftools dependency updated correctly.The bcftools dependency has been updated to use
>=1.19, which addresses the previous review comment. This change allows for more flexibility in version selection while ensuring a minimum version requirement.
14-19: LGTM: pysam installation method updated with clear explanation.The change to install pysam via pip is well-documented and addresses potential version conflicts with snakemake. The comments provide valuable context for this decision.
Note: The indentation appears correct despite the static analysis warning. The pip section is correctly indented at 2 spaces, and its contents at 4 spaces, which is standard for YAML files.
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setup_creators/solutions/08_Snakefile_script2 (1)
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1-65: Overall assessment: Improved workflow organization and functionalityThe changes made to this Snakefile have significantly improved the workflow's organization and functionality. Key improvements include:
- Introduction of a SAMPLES variable for easier sample management.
- Reorganization of output files for better structure.
- Addition of a new visualization step with the 'plot_positions' rule.
- Consistent use of the 'calls/' directory for output files.
These changes align well with the PR objectives of refactoring the Python chapter and introducing the run directive more thoroughly. The workflow is now more coherent and easier to understand.
While the changes are generally positive, consider the suggestions made in previous comments for further improvements:
- Using a configuration file for sample management to increase flexibility.
- Adding error handling and conda environment specifications to plotting rules.
- Using variables for common paths to ease future modifications.
These suggestions could further enhance the robustness and maintainability of the workflow.
slides/creators/Python_in_Snakemake.tex (2)
142-160: Excellent addition of hands-on refactoring and debugging tasksThe new "Refactoring and Debugging" section is a great addition to the course material. It provides learners with practical tasks that reinforce the concepts taught and encourages critical thinking about code organization and debugging.
The tasks are well-structured and cover important aspects such as error correction, code organization, and visualization. This hands-on approach will greatly benefit the learners in understanding and applying the concepts.
418-429: Improved debugging instructions for external scriptsThe updated "Debugging external Scripts" section now includes clear and concise instructions for debugging both Python and R scripts in Snakemake workflows. This is a valuable addition that will help users troubleshoot issues with their external scripts more effectively.
The inclusion of specific commands and techniques for both Python and R demonstrates a thoughtful approach to addressing the needs of users working with different languages in their Snakemake workflows.
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🧹 Outside diff range and nitpick comments (2)
slides/creators/Python_in_Snakemake.tex (2)
120-138: Improved example for therunactionThe revised section provides a more practical and relevant example of using the
runaction. The new example of plotting positions is much more illustrative of real-world usage. The note about indentation is a crucial reminder for Python beginners.Consider adding a brief comment about the ellipsis (...) in the code example to clarify that it represents omitted code, not actual Python syntax.
418-429: Improved debugging instructions for Python and R scriptsThe addition of debugging instructions for both Python and R scripts is very helpful. The mention of the
--debugflag for Python scripts and thesave.image()function for R scripts provides practical solutions for debugging.Consider mentioning any R-specific debugging tools that integrate well with Snakemake, if they exist. This could provide more robust debugging options for R users.
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slides/creators/Python_in_Snakemake.tex (4)
Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-07T18:50:01.657Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-07T18:49:29.039Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-07T18:50:30.670Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-07T18:48:51.479Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.
🔇 Additional comments (6)
slides/creators/Python_in_Snakemake.tex (6)
29-31: Improved clarity in learning objectivesThe expanded objectives provide a clearer roadmap for the content. The use of ellipsis to connect related points is a nice touch, improving readability.
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55-59: Enhanced introduction to Snakemake's APIThe modified introduction provides better context for learners. Encouraging exploration of Snakemake's API before using custom Python code is a good practice that can lead to more efficient and idiomatic use of Snakemake.
142-160: Excellent addition of hands-on refactoring and debugging tasksThis new section provides valuable practical experience for learners. The tasks encourage critical thinking about code organization, error correction, and result visualization. The use of placeholders for paths is consistent with the project's approach and will be correctly rendered during build.
207-217: Clear introduction to thescriptdirectiveThis new section effectively introduces the
scriptdirective and explains its relationship to the Snakefile environment. The explanation of how rule-specific information can be forwarded to scripts is particularly valuable. The connection drawn to the earlierrundirective example helps reinforce the learner's understanding.
472-501: Excellent addition on movingrundirectives to external scriptsThis new section effectively teaches best practices for maintaining clean and manageable Snakefiles. The hands-on task of moving complex
rundirectives to external scripts is a valuable exercise. Providing both guidance and a solution helps learners reinforce their understanding and verify their work.
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1-506: Comprehensive improvements to Python in Snakemake tutorialThe changes to this file significantly enhance its educational value. Key improvements include:
- Clearer learning objectives
- More practical examples of using the
runaction- New sections on using external scripts and the
scriptdirective- Addition of hands-on tasks for refactoring and debugging
- Improved debugging instructions for both Python and R scripts
- Guidance on best practices for maintaining clean Snakefiles
These changes provide a more comprehensive and engaging coverage of Python usage in Snakemake, with a good balance of theory and practical exercises.
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🧹 Outside diff range and nitpick comments (4)
slides/creators/Python_in_Snakemake.tex (4)
120-138: Improved example for therunactionThe new example of using the
runaction for plotting positions provides a more practical and relevant demonstration. This change will help users better understand how to implement Python code directly in their Snakefile.However, there's a small typo that needs correction:
- Imaging this code in our \altverb{Snakefile}: + Imagine this code in our \altverb{Snakefile}:
259-271: Effective hands-on task for using thescriptdirectiveThe new hands-on task for writing a plotting rule using the
scriptdirective is an excellent addition. It provides a practical opportunity for users to apply the concepts they've just learned about external scripts in Snakemake.To further enhance this section:
Consider adding a brief explanation of why using the
scriptdirective might be preferable to including the plotting code directly in the Snakefile. This could help users understand the benefits of this approach in terms of code organization and reusability.
418-429: Clear instructions for debugging external scriptsThe consolidated section on debugging external scripts provides clear and concise instructions for both Python and R scripts. This information will be valuable for users when troubleshooting their Snakemake workflows.
To further enhance this section:
Consider adding a brief example of how to use the
print()orlogging()functions in a Python script within a Snakemake rule. This could help users understand how to implement effective debugging in practice.
491-502: Clear solution for using thescriptdirectiveThe provided solution clearly demonstrates how to implement the
scriptdirective in a Snakemake rule. The reference to additional solution files in the solutions folder is helpful for users who want to compare their work or need more guidance.To further enhance this section:
Consider adding a brief explanation of the benefits of this approach compared to the original
rundirective implementation. This could reinforce the reasons for moving code to external scripts and help users understand the advantages in terms of code organization and maintainability.
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Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-08T17:41:54.542Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-07T18:50:01.657Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-08T17:41:54.542Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-07T18:49:29.039Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-08T17:41:54.542Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-07T18:50:30.670Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-08T17:41:54.542Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-07T18:48:51.479Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.
🔇 Additional comments (6)
slides/creators/Python_in_Snakemake.tex (6)
29-31: Improved clarity in learning objectivesThe updated objectives provide a clearer and more comprehensive overview of the topics to be covered. The use of ellipsis to split the second objective across two lines is a good formatting choice, maintaining readability while conveying the connection between the two parts.
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55-59: Enhanced introduction to Snakemake functionsThe updated content provides a better approach to introducing Snakemake's built-in functions. By encouraging users to explore the Snakemake API first, it helps them understand the available tools before resorting to custom Python code. This change will likely lead to more efficient and idiomatic use of Snakemake.
142-160: Excellent addition of hands-on refactoring and debugging taskThe new hands-on task for refactoring and debugging a Snakefile is an excellent addition to the tutorial. It provides valuable practical experience and encourages critical thinking about file organization and error correction. This task will help users develop important skills for working with Snakemake in real-world scenarios.
207-217: Valuable introduction to thescriptdirectiveThe new section introducing the
scriptdirective is a valuable addition to the tutorial. It explains how to use external Python scripts within Snakemake rules, which is crucial for creating more modular and maintainable workflows. This information will help users better organize their code and leverage the full power of Snakemake's integration with Python.
462-462: Correct use of placeholders for display programThe use of the placeholder
<++cluster.display_program++>for the display program is correct. As per the project's conventions, these placeholders will be automatically replaced with actual values during the build process using Jinja2.
472-487: Excellent guidance on code organization in SnakemakeThe new section on moving code from a
rundirective to an external script provides valuable guidance on best practices for organizing code in Snakemake workflows. It encourages users to think critically about when to use inline code vs. external scripts, which is crucial for maintaining clean and manageable workflows.The hands-on task reinforces these concepts and gives users practical experience in refactoring their Snakemake code. This addition will significantly improve users' understanding of how to structure their Snakemake projects effectively.
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🧹 Outside diff range and nitpick comments (3)
slides/creators/Python_in_Snakemake.tex (3)
120-138: Improved explanation of therunaction with practical exampleThe revised section provides a clearer, more practical demonstration of the
runaction. The new example of plotting positions is more relevant to bioinformatics workflows. The note about preserving indentation is crucial for newcomers to Python.Consider adding a brief explanation of why plotting might be done within a Snakefile rule, to help learners understand when to use the
runaction versus external scripts.
418-429: Improved debugging instructions for external scriptsThe consolidated debugging instructions for both Python and R scripts are a valuable addition. The information about using
print()andlogging()functions for Python scripts is particularly helpful. The addition of R script debugging instructions makes this section more comprehensive.Consider adding a brief note about the importance of removing or commenting out debug statements before finalizing the workflow for production use.
492-502: Clear solution for code organization exerciseThe provided solution clearly demonstrates how to modify the rule to use the
scriptdirective. This helps learners verify their work and reinforces the concept of using external scripts in Snakemake workflows.Consider adding a brief explanation of the benefits of this refactoring (e.g., improved readability, easier maintenance) to reinforce the reasons for this best practice.
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📓 Learnings (1)
slides/creators/Python_in_Snakemake.tex (8)
Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-08T17:41:54.542Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:463-463 Timestamp: 2024-10-07T18:50:01.657Z Learning: In the project, placeholders like '<++cluster.display_program++>' in `slides/creators/Python_in_Snakemake.tex` are intentionally used and will be replaced by values from a configuration file using Jinja2. Do not flag these placeholders as needing replacement.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-08T17:41:54.542Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:262-265 Timestamp: 2024-10-07T18:49:29.039Z Learning: Placeholders like '<++course.pathtosolutions++>' in 'slides/creators/Python_in_Snakemake.tex' are automatically rendered using Jinja2 and replaced with values from a configuration file during the build process.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-08T17:41:54.542Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:157-157 Timestamp: 2024-10-07T18:50:30.670Z Learning: In this project, placeholders like `<++...++>` are rendered using Jinja2 and values from a configuration file, so they should not be replaced manually.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-08T17:41:54.542Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.Learnt from: cmeesters PR: snakemake/snakemake-hpc-teaching-material#158 File: slides/creators/Python_in_Snakemake.tex:171-171 Timestamp: 2024-10-07T18:48:51.479Z Learning: In `slides/creators/Python_in_Snakemake.tex`, the `@` symbols around code are used to indicate characters to be highlighted; they themselves will not be visible on the slides.
🔇 Additional comments (7)
slides/creators/Python_in_Snakemake.tex (7)
29-31: Improved learning objectivesThe updated objectives provide a clearer roadmap for the content, introducing key concepts like the
runaction andscriptdirective. This enhancement will help learners better understand the scope of the material.
55-58: Enhanced introduction to Snakemake functionsThe revised introduction encourages learners to explore Snakemake's API before using custom Python code. This approach promotes better understanding and utilization of Snakemake's built-in capabilities.
207-217: Valuable addition ofscriptdirective explanationThe new section on Snakemake's features for external scripts is a crucial addition. It clearly explains the
scriptdirective and how it relates to theshellandrundirectives. The explanation of how Snakefile information can be accessed within external scripts is particularly useful for creating more modular and maintainable workflows.
472-487: Excellent addition of code organization exerciseThe new section on moving code from a
rundirective to a script is a valuable addition to the course material. It encourages learners to think critically about code organization and promotes best practices in Snakemake workflow development. The discussion about when to use inline code versus external scripts is particularly useful for developing maintainable workflows.The step-by-step instructions for creating the new Python script are clear and should help learners successfully complete the exercise.
Line range hint
1-507: Overall excellent improvements to the Python in Snakemake slidesThe changes made to this file significantly enhance the educational content on using Python in Snakemake. Key improvements include:
- Clearer learning objectives
- More practical examples of using the
runaction andscriptdirective- Addition of hands-on exercises for refactoring and debugging
- Improved explanations of Snakemake's features for external scripts
- Consolidated debugging instructions for both Python and R scripts
- New section on best practices for code organization
These changes provide a more comprehensive and practical learning experience for students working with Snakemake and Python. The material now offers a better balance of theoretical knowledge and hands-on practice, which should lead to improved understanding and retention of the concepts.
259-271: Effective hands-on exercise forscriptdirectiveThis new exercise provides excellent practical experience in using the
scriptdirective. It reinforces the concepts introduced earlier and gives learners a chance to apply their knowledge. The step-by-step instructions are clear and should help learners create a functional plotting rule.Verify that the placeholders are correctly replaced:
#!/bin/bash # Check if the placeholders are correctly replaced in the final rendered document grep -n '<++course\.pathtosolutions++>' slides/creators/Python_in_Snakemake.tex
462-462: Flexible output visualization instructionThe use of a placeholder for the display program allows for easy customization based on the specific cluster environment. This change enhances the portability of the teaching material across different systems.
Verify that the placeholder is correctly replaced:
#!/bin/bash # Check if the placeholder is correctly replaced in the final rendered document grep -n '<++cluster\.display_program++>' slides/creators/Python_in_Snakemake.tex
should refactor the python chapter
Summary by CodeRabbit
New Features
scriptdirective to execute external scripts within Snakemake workflows.seabornadded for enhanced data visualization.Bug Fixes
Documentation