From 8b7a3f6bb3fcf4b88a573149200bf16edaa3b2b6 Mon Sep 17 00:00:00 2001
From: Deepika Yeramosu <94006622+dyeramosu@users.noreply.github.com>
Date: Fri, 14 Jul 2023 16:23:16 -0400
Subject: [PATCH] Made runtime attrs to args in MT pipeline  (#8417)

---
 scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
index 4c0dcc8c19c..64bf40f3c3f 100644
--- a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
+++ b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
@@ -21,6 +21,8 @@ workflow AlignmentPipeline {
 
     #Optional runtime arguments
     Int? preemptible_tries
+    Int disk_size = ceil(size(input_bam, "GB") * 4 + size(mt_fasta, "GB") + size(mt_fasta_index, "GB") + size(mt_amb, "GB") + size(mt_ann, "GB") + size(mt_bwt, "GB") + size(mt_pac, "GB") + size(mt_sa, "GB")) + 20
+    Int mem = 6
   }
 
   parameter_meta {
@@ -43,7 +45,9 @@ workflow AlignmentPipeline {
       ref_bwt = mt_bwt,
       ref_pac = mt_pac,
       ref_sa = mt_sa,
-      preemptible_tries = preemptible_tries
+      preemptible_tries = preemptible_tries,
+      disk_size = disk_size,
+      mem = mem
   }
 
   output {
@@ -72,8 +76,8 @@ task AlignAndMarkDuplicates {
 
     # runtime
     Int? preemptible_tries
-    Int disk_size = ceil(size(input_bam, "GB") * 4 + size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_amb, "GB") + size(ref_ann, "GB") + size(ref_bwt, "GB") + size(ref_pac, "GB") + size(ref_sa, "GB")) + 20
-    Int mem = 6
+    Int disk_size
+    Int mem
   }
 
   String basename = basename(input_bam, ".bam")