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Fix error thrown at genmod models
This is the error thrown: https://github.com/moonso/genmod/blob/master/genmod/commands/annotate_models.py#L185
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workflow/rules/genmod_models.smk

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@ rule genmod_models:
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refgenome = expand("{refgenome}", refgenome = config['REFGENOME'])
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output:
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protected("../results/annotated/{sample}_filtered_annotated.vcf")
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params:
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"--vep"
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log:
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"logs/genmod_models/{sample}.log"
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benchmark:
@@ -15,4 +17,4 @@ rule genmod_models:
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message:
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"Annotating {input.vcf} with patterns of inheritance"
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shell:
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"genmod models {input.vcf} -f {input.pedigree} -o {output} -p {threads} &> {log}"
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"genmod models {input.vcf} -f {input.pedigree} -o {output} {params} -p {threads} &> {log}"

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