feat: GATK Meta-wrapper update to follow pathvars #4666
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meta/bio/gatk_mutect2_calling/test/reference/known.vcf.gzis excluded by!**/*.gz
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meta/bio/gatk_mutect2_calling/meta.yaml(1 hunks)meta/bio/gatk_mutect2_calling/meta_wrapper.smk(6 hunks)meta/bio/gatk_mutect2_calling/test/Snakefile(1 hunks)meta/bio/gatk_mutect2_calling/test/config.yaml(1 hunks)test_wrappers.py(1 hunks)
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test_wrappers.py
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test_wrappers.py (1)
6562-6562: LGTM! Test path correctly updated to reflect new structure.The path change from
variant/Sample1.filtered.vcf.gz.tbitoresults/variant/Sample1.filtered.vcf.gz.tbicorrectly aligns with the new pathvars-based output structure defined in the meta-wrapper.meta/bio/gatk_mutect2_calling/test/config.yaml (1)
1-9: LGTM! Configuration properly defines all required pathvars.The pathvars configuration is complete and consistent with the documentation in
meta.yaml. The per-sample templating using"{sample}"for theperpathvar and"mapped/{sample}.bam"forbam_filecorrectly enables flexible path resolution across the workflow.meta/bio/gatk_mutect2_calling/test/Snakefile (1)
6-11: LGTM! Snakefile correctly adopts config-driven meta-wrapper pattern.The addition of the
configfiledirective and the conversion to nestedmeta_wrapperblock form are both correct. This enables the workflow to use the pathvars defined inconfig.yamlfor flexible path resolution.meta/bio/gatk_mutect2_calling/meta_wrapper.smk (1)
3-158: Verify hardcoded{sample}references in params are intentional.The conversion to placeholders looks comprehensive and consistent. However, Lines 42 and 77 contain
{sample}directly in theextraparams strings:
- Line 42:
"--RGLB lib1 --RGPL illumina --RGPU {sample} --RGSM {sample}"- Line 77:
" --tumor-sample {sample} "This creates an implicit constraint that the
perpathvar must be exactly"{sample}". If users configureperas"{sample_id}"or another pattern, these params would not expand correctly.Consider either:
- Documenting this constraint in
meta.yaml, or- Making it more flexible by using the
<per>placeholder in params where appropriate
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This PR lets GATK meta-wrapper use
pathvarssyntax.QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Tests