fix: typo on samtools regions file

[fgvieira]

Fix typo on samtools option.

Summary by CodeRabbit

• Bug Fixes
  • Updated error messaging for region file arguments to support both singular and plural forms.
  • Aligned the command option construction with the revised messaging for improved clarity.
  • Simplified logic for appending thread options to enhance flexibility.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request modifies the get_samtools_opts function in the samtools wrapper utility. It updates the error message related to region file handling by using a regex-like notation (--region[s]-file) to indicate that both singular and plural forms are acceptable. Additionally, the option construction is updated to use --region-file instead of the previously hardcoded --regions-file. No changes have been made to any exported or public entities.

Changes

File(s)	Change Summary
snakemake_wrapper_utils/samtools.py	Updated error messaging to use --region[s]-file for flexibility and modified the samtools options construction to use --region-file instead of --regions-file.

Sequence Diagram(s)

sequenceDiagram
    participant Caller as Caller
    participant Utils as get_samtools_opts
    Caller->>Utils: Call get_samtools_opts(params.extra)
    alt Invalid region file argument in params.extra
        Utils->>Caller: Raise error ("Use '--region[s]-file' instead of '--regions-file'")
    else Valid or no conflict
        Utils->>Utils: Construct samtools_opts using "--region-file"
        Utils->>Caller: Return constructed samtools_opts string
    end

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Possibly related PRs

• feat: parse samtools regions #40: The changes in the main PR and the retrieved PR are related as both modify the get_samtools_opts function in snakemake_wrapper_utils/samtools.py, specifically addressing the handling of region file options and error messages.

Suggested reviewers

• johanneskoester

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 4a41162 and bcce33a.

📒 Files selected for processing (1)

• snakemake_wrapper_utils/samtools.py (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• snakemake_wrapper_utils/samtools.py

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