feat: add wrapper for rbt vcf_fix_iupac_alleles

[fgvieira]

Description

QC

• I confirm that:

For all wrappers added by this PR,

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.
• Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

[johanneskoester]

Why the sort? rbt vcf-fix-iupac-alleles does not change the order of the records.

[fgvieira]

The main idea was to allow for automatic output on any format (bcf, vcf, vcf.gz).
Since I was using it to standardize resources (known variation from ensembl), I thought that sort would be a nice-to-have (just to be sure the output was sorted) and the extra runtime would be ok since it would only be run once.

But I can also remove it (or switch to view), if you prefer to keep the wrapper more general.

[fgvieira]

Ping @johanneskoester

[github-actions]

This PR was marked as stale because it has been open for 6 months with no activity.

[github-actions]

This PR was marked as stale because it has been open for 6 months with no activity.

[github-actions]

This PR was marked as stale because it has been open for 6 months with no activity.

[coderabbitai]

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📥 Commits

Reviewing files that changed from the base of the PR and between 827ac09 and 612926d.

⛔ Files ignored due to path filters (1)

• bio/rbt/vcf_fix_iupac_alleles/test/homo_sapiens-chrMT.vcf.gz is excluded by !**/*.gz

📒 Files selected for processing (5)

• bio/rbt/vcf_fix_iupac_alleles/environment.yaml (1 hunks)
• bio/rbt/vcf_fix_iupac_alleles/meta.yaml (1 hunks)
• bio/rbt/vcf_fix_iupac_alleles/test/Snakefile (1 hunks)
• bio/rbt/vcf_fix_iupac_alleles/wrapper.py (1 hunks)
• test.py (1 hunks)

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