docs: Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease by rohan-ibn-tariq · Pull Request #3605 · snakemake/snakemake

rohan-ibn-tariq · 2025-05-27T13:49:38Z

Updated docs with recent version of the wrapper for the rule samtools_index and used this rule because it is easy to follow and also consistent with the previous step, automatic deployment of software dependencies.
Fixes #3585

Summary by CodeRabbit

Documentation
- Updated the tutorial example to demonstrate the use of a samtools indexing wrapper instead of a BWA mapping wrapper.
- Revised input, output, log, params, and wrapper directives in the example for clarity and accuracy.
- Added a conda environment specification for samtools in the example.

…ex and used this rule because easy to follow and also consistent with previous step, automatic deployment of software dependencies. Fixes snakemake#3585

coderabbitai · 2025-05-27T13:49:45Z

📝 Walkthrough

Walkthrough

The documentation tutorial was updated to replace the example Snakemake rule from bwa_mem to samtools_index, updating all associated directives and code to match the new use case. The wrapper path, input, output, parameters, log, and conda environment were all modified accordingly.

Changes

File(s)	Change Summary
docs/tutorial/additional_features.rst	Updated example rule from `bwa_mem` to `samtools_index`, revised all directives and wrapper details

Assessment against linked issues

Objective	Addressed	Explanation
Update outdated example code and wrapper reference in tutorial (Issue #3585)	✅

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coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

docs/tutorial/additional_features.rst (1)
178-190: Review wrapper code snippet syntax and version tag
The new wrapper example effectively demonstrates input, output, conda, log, params, and wrapper directives for samtools_index.
Nitpick: remove the trailing comma after the log path to avoid confusion:
-    log:
-        "logs/samtools_index/{sample}.log",
+    log:
+        "logs/samtools_index/{sample}.log"
Please verify that the wrapper version v6.2.0 exists in the Snakemake wrapper repository.

📜 Review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 5f04aea and 4cdb7e9.

📒 Files selected for processing (1)

docs/tutorial/additional_features.rst (1 hunks)

🔇 Additional comments (1)

docs/tutorial/additional_features.rst (1)

174-174: Introduction for wrapper example is clear
The updated sentence properly introduces the samtools_index wrapper example in context.

🤖 I have created a release *beep* *boop* --- ## [9.6.0](v9.5.1...v9.6.0) (2025-06-16) ### Features * Prefer papermill to nbconvert ([#2857](#2857)) ([4263b03](4263b03)) ### Bug Fixes * DeprecationWarning when using snakemake.utils.validate ([#3420](#3420)) ([cf72427](cf72427)) * display group jobs on dryrun ([#3435](#3435)) ([3bebef4](3bebef4)) * expandvars for special profile keys ([#3597](#3597)) ([4020188](4020188)) * fix bug causing --precommand to not being executed before each remote job ([#3625](#3625)) ([e59d125](e59d125)) * improved toggle switch behavior in reports ([#3623](#3623)) ([0c4bd23](0c4bd23)) * pass envvars defined via the envvars directive to remote jobs ([#3626](#3626)) ([d4890b4](d4890b4)) * remove wms arg, update logging cli docs ([#3622](#3622)) ([3a9a5ac](3a9a5ac)) * typo in CondaEnvDirSpec.__eq__ (issue [#3192](#3192)) ([#3613](#3613)) ([f4c107f](f4c107f)) * Unclear handling of params overriding with inheritance ([#3624](#3624)) ([077ac4a](077ac4a)) ### Documentation * Added snakemake command to execute the rule plot_with_python ([#3608](#3608)) ([bd99c11](bd99c11)) * Updated Reporting Section of The Tutorial(Interaction, Visualization, and Reporting with Snakemake) ([#3606](#3606)) ([91e90ba](91e90ba)) * Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually ([#3607](#3607)) ([3bd114b](3bd114b)) * Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease ([#3605](#3605)) ([b3bcc21](b3bcc21)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

…nsistency & Ease (snakemake#3605) Updated docs with recent version of the wrapper for the rule samtools_index and used this rule because it is easy to follow and also consistent with the previous step, automatic deployment of software dependencies. Fixes snakemake#3585  ## Summary by CodeRabbit - **Documentation** - Updated the tutorial example to demonstrate the use of a samtools indexing wrapper instead of a BWA mapping wrapper. - Revised input, output, log, params, and wrapper directives in the example for clarity and accuracy. - Added a conda environment specification for samtools in the example.  Co-authored-by: rohan-ibn-tariq <your-username@users.noreply.github.com>

🤖 I have created a release *beep* *boop* --- ## [9.6.0](snakemake/snakemake@v9.5.1...v9.6.0) (2025-06-16) ### Features * Prefer papermill to nbconvert ([snakemake#2857](snakemake#2857)) ([4263b03](snakemake@4263b03)) ### Bug Fixes * DeprecationWarning when using snakemake.utils.validate ([snakemake#3420](snakemake#3420)) ([cf72427](snakemake@cf72427)) * display group jobs on dryrun ([snakemake#3435](snakemake#3435)) ([3bebef4](snakemake@3bebef4)) * expandvars for special profile keys ([snakemake#3597](snakemake#3597)) ([4020188](snakemake@4020188)) * fix bug causing --precommand to not being executed before each remote job ([snakemake#3625](snakemake#3625)) ([e59d125](snakemake@e59d125)) * improved toggle switch behavior in reports ([snakemake#3623](snakemake#3623)) ([0c4bd23](snakemake@0c4bd23)) * pass envvars defined via the envvars directive to remote jobs ([snakemake#3626](snakemake#3626)) ([d4890b4](snakemake@d4890b4)) * remove wms arg, update logging cli docs ([snakemake#3622](snakemake#3622)) ([3a9a5ac](snakemake@3a9a5ac)) * typo in CondaEnvDirSpec.__eq__ (issue [snakemake#3192](snakemake#3192)) ([snakemake#3613](snakemake#3613)) ([f4c107f](snakemake@f4c107f)) * Unclear handling of params overriding with inheritance ([snakemake#3624](snakemake#3624)) ([077ac4a](snakemake@077ac4a)) ### Documentation * Added snakemake command to execute the rule plot_with_python ([snakemake#3608](snakemake#3608)) ([bd99c11](snakemake@bd99c11)) * Updated Reporting Section of The Tutorial(Interaction, Visualization, and Reporting with Snakemake) ([snakemake#3606](snakemake#3606)) ([91e90ba](snakemake@91e90ba)) * Updated Requirement Section of The Tutorial With Warning of Not Installing The Tools Manually ([snakemake#3607](snakemake#3607)) ([3bd114b](snakemake@3bd114b)) * Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease ([snakemake#3605](snakemake#3605)) ([b3bcc21](snakemake@b3bcc21)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

updated docs with recent version of wrapper for the rule samtools_ind…

4cdb7e9

…ex and used this rule because easy to follow and also consistent with previous step, automatic deployment of software dependencies. Fixes snakemake#3585

rohan-ibn-tariq requested a review from johanneskoester as a code owner May 27, 2025 13:49

rohan-ibn-tariq changed the title ~~Updated Wrapper Use in Tutorial and Simple Rule For Consistency & Ease~~ docs: Updated Wrapper Use in Tutorial and Simple Rule For Consistency & Ease May 27, 2025

rohan-ibn-tariq changed the title ~~docs: Updated Wrapper Use in Tutorial and Simple Rule For Consistency & Ease~~ docs: Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease May 27, 2025

coderabbitai Bot reviewed May 27, 2025

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johanneskoester approved these changes Jun 11, 2025

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johanneskoester merged commit b3bcc21 into snakemake:main Jun 12, 2025
49 of 51 checks passed

snakemake-bot mentioned this pull request Jun 12, 2025

chore(main): release 9.6.0 #3611

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docs: Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease#3605

docs: Updated Wrapper Version in Tutorial and Used Simple Rule For Consistency & Ease#3605
johanneskoester merged 1 commit into
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rohan-ibn-tariq:update_tutorial_with_latest_wrapper_example_for_samtools

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