Fixed improper use of --loop-cats flag

Tuks-ICMM · Jan 7, 2021 · 8ef4e26 · 8ef4e26
1 parent 6050c79
commit 8ef4e26
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/Snakefile b/Snakefile
@@ -255,7 +255,8 @@ rule ALL_ANALYZE_SUPER:
 
     run:
         shell("module load plink-2; plink2 --vcf {input.vcf} --freq --export vcf-4.2 bgz --out final/SUPER/{params.prefix}"),
-        shell("module load plink-2; plink2 --vcf {input.vcf} --double-id --within {input.popClusters} --freq --missing --indep-pairwise 50 5 .05 --hardy midp --loop-cats --out final/SUPER/{params.prefix}"),
+        for pop in superPop:
+            shell("module load plink-2; plink2 --vcf {input.vcf} --double-id --within {input.popClusters} --freq --missing --indep-pairwise 50 5 .05 --hardy midp --loop-cats {pop} --out final/SUPER/{params.prefix}"),
 
 
 rule ALL_ANALYZE_SUB:
@@ -281,7 +282,8 @@ rule ALL_ANALYZE_SUB:
 
     run:
         shell("module load plink-2; plink2 --vcf {input.vcf} --freq --export vcf-4.2 bgz --out final/SUB/{params.prefix}"),
-        shell("module load plink-2; plink2 --vcf {input.vcf} --double-id --within {input.popClusters} --freq --missing --indep-pairwise 50 5 .5 --hardy midp --loop-cats --out final/SUB/{params.prefix}"),
+        for pop in subPop:
+            shell("module load plink-2; plink2 --vcf {input.vcf} --double-id --within {input.popClusters} --freq --missing --indep-pairwise 50 5 .5 --hardy midp --loop-cats {pop} --out final/SUB/{params.prefix}"),
 
 # Add in VEP API calls
 rule ALL_VEP: