docs: updated for passing commands as script

[cmeesters]

This PR merely updates the documentation section and describes the --slurm-pass-command-as-script flag.

Summary by CodeRabbit

• Documentation
  • Updated SLURM configuration documentation with details on the --slurm-pass-command-as-script option for submitting job commands via temporary shell scripts.

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[coderabbitai]

Walkthrough

Added documentation for the --slurm-pass-command-as-script feature, explaining that it submits job commands via temporary shell scripts to sbatch instead of using the --wrap option, helping overcome SLURM submit line length limitations.

Changes

Cohort / File(s)	Change Summary
SLURM Script Submission Documentation docs/further.md	Added sections describing the --slurm-pass-command-as-script feature, explaining how it delegates job command content to a script file to work around SLURM submit line length or character limits imposed by slurm_max_submit_line_size

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Possibly related PRs

• feat: pass a shell script to sbatch rather than the command directly #380: Implements the --slurm-pass-command-as-script feature in code that this documentation describes
• docs: review and edit new docs #237: Also modifies docs/further.md with broader SLURM documentation updates
• docs: rewrite of the documentation  #219: Also modifies docs/further.md and covers SLURM job submission via scripts

Suggested reviewers

• dlaehnemann
• DrYak

Poem

🐰 A rabbit hops through further.md with glee,
Scripting secrets for sbatch to see!
No line length limits shall hold us back,
With scripts so swift on the SLURM attack! ✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly describes the main change: documentation updates about passing commands as a script, which aligns with the PR objective and the changes made to docs/further.md.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch docs/passing_as_script

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (2)

docs/further.md (2)

257-262: Improve clarity with usage examples and temporary script lifecycle.

The documentation explains the purpose and motivation clearly, but could be enhanced with practical details:

1. Add a command-line usage example showing how to enable the flag (e.g., snakemake --executor slurm --slurm-pass-command-as-script ...)
2. Briefly mention the lifecycle of temporary scripts—are they cleaned up automatically after job completion?
3. Consider adding a concrete scenario when users would hit the line length limits in practice.

These additions would help users understand when and how to use this feature.

---

257-257: Consider consistent flag formatting in section headings.

The section heading uses backticks around the flag name (--slurm-pass-command-as-script), whereas nearby sections like "slurm_partition" (line 239) and "slurm_account" (line 245) use plain text without backticks. For consistency with the surrounding documentation style, consider removing the backticks:

-##### Passing Commands as Scripts: `--slurm-pass-command-as-script`
+##### Passing Commands as Scripts

Or, if you prefer to keep the flag name emphasized, consider using bold instead:

-##### Passing Commands as Scripts: `--slurm-pass-command-as-script`
+##### Passing Commands as Scripts: **--slurm-pass-command-as-script**

📜 Review details

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Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between ccde8ca and 55ddecd.

📒 Files selected for processing (1)

• docs/further.md (1 hunks)

🧰 Additional context used

🧠 Learnings (5)

📓 Common learnings

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 187
File: .github/workflows/post_to_mastodon.yml:0-0
Timestamp: 2025-01-17T17:27:32.446Z
Learning: In the mastodon publishing workflow for snakemake-executor-plugin-slurm, the PR_TITLE environment variable is required by the post_to_mastodon.sh script and should be preserved.

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 0
File: :0-0
Timestamp: 2025-01-13T09:54:22.950Z
Learning: PR #173 (adding gres resource specification) depends on PR #28 in snakemake-executor-plugin-slurm-jobstep repository, as changes were required in the cpu-settings function of the jobstep-Executor module.

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 0
File: :0-0
Timestamp: 2025-09-09T15:55:55.669Z
Learning: In the Snakemake SLURM executor plugin, Snakemake submits itself as a job using the --wrap parameter in the sbatch command, rather than creating or submitting a separate job.sh script file. The actual implementation uses `call += f' --wrap="{exec_job}"'` where exec_job is the formatted snakemake execution command.

📚 Learning: 2025-09-09T15:55:55.669Z

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 0
File: :0-0
Timestamp: 2025-09-09T15:55:55.669Z
Learning: In the Snakemake SLURM executor plugin, Snakemake submits itself as a job using the --wrap parameter in the sbatch command, rather than creating or submitting a separate job.sh script file. The actual implementation uses `call += f' --wrap="{exec_job}"'` where exec_job is the formatted snakemake execution command.

Applied to files:

• docs/further.md

📚 Learning: 2025-03-31T11:52:05.373Z

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 249
File: snakemake_executor_plugin_slurm/submit_string.py:21-29
Timestamp: 2025-03-31T11:52:05.373Z
Learning: In the snakemake-executor-plugin-slurm project, account and partition parameters are validated in the submit function before reaching the get_submit_command function. By design, these parameters are either empty strings or already properly formatted with SLURM parameter tags, making additional validation in get_submit_command unnecessary.

Applied to files:

• docs/further.md

📚 Learning: 2025-03-10T13:34:59.270Z

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 173
File: tests/tests.py:79-86
Timestamp: 2025-03-10T13:34:59.270Z
Learning: In the Snakemake executor plugin for SLURM, all GPU resources (even simple numeric ones) should be translated to the `--gpus` flag (plural) to match SLURM's expectations, not `--gpu` (singular).

Applied to files:

• docs/further.md

📚 Learning: 2025-03-10T13:34:59.270Z

Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 173
File: tests/tests.py:79-86
Timestamp: 2025-03-10T13:34:59.270Z
Learning: In the Snakemake executor plugin for SLURM, all GPU resources (both simple numeric values and model:number specifications) should be translated to the `--gpus` flag (plural form) to match SLURM's command line interface expectations.

Applied to files:

• docs/further.md

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• GitHub Check: testing

🔇 Additional comments (1)

docs/further.md (1)

259-261: Technical accuracy and placement look good.

The explanation of the feature—how it works and why it exists—is clear and accurate. The section placement within the SLURM-specific resources documentation is appropriate, and the terminology aligns well with the existing content.