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docs: fixed wrong code example for collect() function#4037

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johanneskoester merged 1 commit intosnakemake:mainfrom
SrPeter128:fix_docu_issue_collect_function
Mar 10, 2026
Merged

docs: fixed wrong code example for collect() function#4037
johanneskoester merged 1 commit intosnakemake:mainfrom
SrPeter128:fix_docu_issue_collect_function

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@SrPeter128 SrPeter128 commented Mar 10, 2026

A very small PR fixing a wrong code example in the docs.
collect() function takes the keyword "item", not "sample". The minimal example of the issue #3541 has been reproduced and the problem was confirmed.

Fix #3541

Summary by CodeRabbit

  • Documentation
    • Updated example documentation for collect rules to demonstrate proper parameter binding when using lookup results. Example now shows how to correctly reference bound values in subsequent wildcards.

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coderabbitai bot commented Mar 10, 2026

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 7071c257-4a56-4e57-ac2a-c0b91c992175

📥 Commits

Reviewing files that changed from the base of the PR and between b88171c and 60ffb6b.

📒 Files selected for processing (1)
  • docs/snakefiles/rules.rst

📝 Walkthrough

Walkthrough

Documentation example corrected to use item=lookup(...) instead of sample=lookup(...) in a collect() rule pattern. This aligns the parameter binding name with the wildcard reference {item.sample} used in the collection path pattern.

Changes

Cohort / File(s) Summary
Documentation Fix
docs/snakefiles/rules.rst
Corrected parameter name in lookup() example from sample= to item= to match the wildcard placeholder in the collect() pattern.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name Status Explanation Resolution
Description check ❓ Inconclusive The description clearly states the issue and references the linked issue #3541, but the QC checklist is not completed as required by the template. Complete the QC checklist by checking the boxes to confirm test coverage and documentation updates are addressed.
✅ Passed checks (4 passed)
Check name Status Explanation
Title check ✅ Passed The title clearly summarizes the main change: fixing a wrong code example in the documentation for the collect() function.
Linked Issues check ✅ Passed The PR directly addresses the requirement from issue #3541 by correcting the documentation example to use 'item' instead of 'sample' as the keyword parameter for collect().
Out of Scope Changes check ✅ Passed The PR makes a focused, minimal change to fix the documented code example, which is directly aligned with the scope of issue #3541 without introducing unrelated changes.
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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@johanneskoester johanneskoester merged commit 5c85ed8 into snakemake:main Mar 10, 2026
60 checks passed
@SrPeter128 SrPeter128 deleted the fix_docu_issue_collect_function branch March 10, 2026 15:43
johanneskoester pushed a commit that referenced this pull request Mar 13, 2026
🤖 I have created a release *beep* *boop*
---


##
[9.17.0](v9.16.3...v9.17.0)
(2026-03-13)


### Features

* Allow storing snakemake metadata in files or databases
([#4012](#4012))
([dd75f31](dd75f31))
* Allow to specify comparison command per-unit test
([#3956](#3956))
([b88171c](b88171c))
* job table orderd topological when run is started
([#4018](#4018))
([75cf506](75cf506))
* lambda functions for priority in rules
([#3253](#3253))
([d2aa226](d2aa226))
* Make on... directive of modules accessible
([#4050](#4050))
([e9f2e1c](e9f2e1c))


### Bug Fixes

* adjust conda tests to not fail on apple silicon; fix
[#4040](#4040)
([#4049](#4049))
([f5b0142](f5b0142))
* allow "--containerize apptainer" to output apptainer format instead of
dockerfile ([#4030](#4030))
([f5cac30](f5cac30))
* apptainer command not recognized when singularity is absent
([#4010](#4010))
([b8162e2](b8162e2))
* capture stderr when tests fail
([#3995](#3995))
([97d74ba](97d74ba))
* **docs:** make Data-dependent conditional execution a complete example
([#4043](#4043))
([3a1d7f2](3a1d7f2))
* don't build the DAG when running unlock. Fixes
[#4000](#4000) and
[#198](#198)
([#4007](#4007))
([acf79fd](acf79fd))
* Ensure pixi tasks may be run as advertised
([#4046](#4046))
([88253c2](88253c2))
* fix checkpoint handling corner cases
([#3870](#3870) and
[#3559](#3559))
([#4015](#4015))
([63f4257](63f4257))
* issue 3642
([#4054](#4054))
([76e6fc2](76e6fc2))
* issue 3815
([#4026](#4026))
([b0eec96](b0eec96))
* logging None in shellcmd context causes error
([#4064](#4064))
([d0652cd](d0652cd))
* lookup function returns default value for empty DataFrame queries
([#4056](#4056))
([f71de97](f71de97))
* make `cache: omit-software` a rule specific property
([#4085](#4085))
([034a9e7](034a9e7))
* reduce number of tests leaving temporary files behind
([#4033](#4033))
([a3a1c97](a3a1c97))
* regression in dynamic resource handling
([#4038](#4038))
([f2c554a](f2c554a))
* somewhat shorter announce message
([#4080](#4080))
([57efc71](57efc71))


### Performance Improvements

* switch reretry with tenacity; decouple container classes (with Python
3.7 compat for old scripts) from rest of the codebase (enabling moving
to newer python versions)
([#4032](#4032))
([ffb19e7](ffb19e7))


### Documentation

* Add AI-assisted contributions policy to contributing guidelines
([#4051](#4051))
([dd70526](dd70526))
* **codebase:** Update & simplify plugin architecture section
([#4052](#4052))
([176cf63](176cf63))
* Correct workflow.source_path() description in documentation
([#4036](#4036))
([45883c5](45883c5))
* fixed wrong code example for collect() function
([#4037](#4037))
([5c85ed8](5c85ed8))
* Minor docs improvements
([#4089](#4089))
([29ea226](29ea226))
* switch to sphinx_design for tabs
([#3976](#3976))
([9674614](9674614))
* typo in the migration table breaking a pip install command
([#4024](#4024))
([66f9dda](66f9dda))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).
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Documentation error: incorrect varible name in example for lookup()

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