From 7bb5c4564de3fbd8af768b671fdde771ebd33df8 Mon Sep 17 00:00:00 2001
From: Danny Park <dpark@broadinstitute.org>
Date: Fri, 29 May 2020 15:03:35 -0400
Subject: [PATCH 1/2] bump dx_instance_type for rmdup_ubam due to picard memory
 requirements

---
 pipes/WDL/tasks/tasks_read_utils.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl
index 4dd59d4e2..6979653d1 100644
--- a/pipes/WDL/tasks/tasks_read_utils.wdl
+++ b/pipes/WDL/tasks/tasks_read_utils.wdl
@@ -109,7 +109,7 @@ task rmdup_ubam {
     memory: select_first([machine_mem_gb, 7]) + " GB"
     cpu:    2
     disks:  "local-disk 375 LOCAL"
-    dx_instance_type: "mem1_ssd1_v2_x2"
+    dx_instance_type: "mem2_ssd1_v2_x2"
   }
 }
 

From f1b5eb6825fdbfc07203995210771fd79c562a1e Mon Sep 17 00:00:00 2001
From: Danny Park <dpark@broadinstitute.org>
Date: Fri, 29 May 2020 15:06:36 -0400
Subject: [PATCH 2/2] --taxIDs for filter_bam_to_taxa wasnt working as is,
 convert to xargs based input

---
 pipes/WDL/tasks/tasks_metagenomics.wdl | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/pipes/WDL/tasks/tasks_metagenomics.wdl b/pipes/WDL/tasks/tasks_metagenomics.wdl
index 3c99b0bd2..9e2d94384 100644
--- a/pipes/WDL/tasks/tasks_metagenomics.wdl
+++ b/pipes/WDL/tasks/tasks_metagenomics.wdl
@@ -665,11 +665,16 @@ task filter_bam_to_taxa {
 
     touch taxfilterargs
     TAXNAMELIST="${write_lines(select_first([taxonomic_names, []]))}"
-    if [ -n "$(cat $TAXNAMELIST)" ]; then echo "--taxNames" >> taxfilterargs; fi
+    if [ -n "$(cat $TAXNAMELIST)" ]; then
+      echo "--taxNames" >> taxfilterargs
+    fi
     cat $TAXNAMELIST >> taxfilterargs
 
-    TAX_IDs="${sep=' ' taxonomic_ids}"
-    if [ -n "$TAX_IDs" ]; then TAX_IDs="--taxIDs $TAX_IDs"; fi
+    TAXIDLIST="${write_lines(select_first([taxonomic_ids, []]))}"
+    if [ -n "$(cat $TAXIDLIST)" ]; then
+      echo "--taxIDs" >> taxfilterargs
+    fi
+    cat $TAXIDLIST >> taxfilterargs
 
     metagenomics.py --version | tee VERSION
 
@@ -681,7 +686,6 @@ task filter_bam_to_taxa {
       "${out_basename}.bam" \
       nodes.dmp \
       names.dmp \
-      $TAX_IDs \
       ${true='--exclude' false='' exclude_taxa} \
       ${true='--without-children' false='' withoutChildren} \
       ${'--minimum_hit_groups=' + minimum_hit_groups} \