diff --git a/myco_cleaned.wdl b/myco_cleaned.wdl
index b9ce254..1c16579 100644
--- a/myco_cleaned.wdl
+++ b/myco_cleaned.wdl
@@ -17,8 +17,6 @@ workflow myco {
 		File?   input_tree
 		Int     min_coverage = 10
 		File?   ref_genome_for_tree_building
-		Int     subsample_cutoff       =  450
-		Int     subsample_seed         = 1965
 		Int     timeout_variant_caller =  120
 	}
 
diff --git a/myco_cleaned_1samp.wdl b/myco_cleaned_1samp.wdl
index a6a524f..808192b 100644
--- a/myco_cleaned_1samp.wdl
+++ b/myco_cleaned_1samp.wdl
@@ -18,11 +18,13 @@ workflow myco_cleaned_one_sample {
     input {
         File decontaminated_fastq_1
         File decontaminated_fastq_2
+        File typical_tb_masked_regions
     }
 
     call WF.myco {
         input:
-            paired_decontaminated_fastq_sets = [[decontaminated_fastq_1, decontaminated_fastq_2]]
+            paired_decontaminated_fastq_sets = [[decontaminated_fastq_1, decontaminated_fastq_2]],
+            typical_tb_masked_regions = typical_tb_masked_regions
     }
 
 output {