From 1edefe688d5997ab29668ab395a4deb218ba2f77 Mon Sep 17 00:00:00 2001
From: Ash O'Farrell <aofarrel@ucsc.edu>
Date: Tue, 18 Apr 2023 14:41:10 -0700
Subject: [PATCH] Fix myco_cleaned inputs

---
 myco_cleaned.wdl       | 2 --
 myco_cleaned_1samp.wdl | 4 +++-
 2 files changed, 3 insertions(+), 3 deletions(-)

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 2727b4a..b6bd9d5 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 {