Update cosigt.smk for the last docker

Author: raveancic

cosigt_smk/workflow/rules/cosigt.smk

@@ -23,7 +23,7 @@ rule cosigt_genotype:
 		prefix="results/cosigt_results/{sample}"
 	shell:
 		'''
-		cosigt {input.zpath} {input.xpack} resources/extra/bad_samples.txt {params.prefix}
+		cosigt -p {input.zpath} -g {input.xpack} -b resources/extra/bad_samples.txt -o {params.prefix}
 		'''
 
 rule evaluate_cosigt:
@@ -95,4 +95,4 @@ rule plot_evaluation_dendro_jaccard:
 	shell:
 		'''
 		python workflow/scripts/tpr.py results/cosigt_results {input.proxi} {output}
-		'''
+		'''