From dfa59a4d356b3fdbf5f5b1b6303be261a73971e9 Mon Sep 17 00:00:00 2001
From: Morgan Taylor <marymorg@broadinstitute.org>
Date: Thu, 25 Feb 2021 13:58:15 -0500
Subject: [PATCH 1/3] reduce memory for ImportGenomes and add this branch to
 dockstore yml

---
 .dockstore.yml                             | 1 +
 scripts/variantstore/wdl/ImportGenomes.wdl | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.dockstore.yml b/.dockstore.yml
index 0b9c4858a2b..7ee538df647 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -57,6 +57,7 @@ workflows:
        branches:
          - master
          - ah_var_store
+         - mmt_reduce_mem
    - name: funcotator
      subclass: WDL
      primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl
diff --git a/scripts/variantstore/wdl/ImportGenomes.wdl b/scripts/variantstore/wdl/ImportGenomes.wdl
index 962dfe5ce03..fccfdc4552c 100644
--- a/scripts/variantstore/wdl/ImportGenomes.wdl
+++ b/scripts/variantstore/wdl/ImportGenomes.wdl
@@ -210,10 +210,10 @@ task CreateImportTsvs {
   >>>
   runtime {
       docker: docker
-      memory: "10 GB"
+      memory: "3.75 GB"
       disks: "local-disk " + disk_size + " HDD"
       preemptible: select_first([preemptible_tries, 5])
-      cpu: 2
+      cpu: 1
   }
   output {
       String done = "true"

From d4907250fcbaf341d6b6f84c5ef92820be7d4f34 Mon Sep 17 00:00:00 2001
From: Morgan Taylor <marymorg@broadinstitute.org>
Date: Tue, 2 Mar 2021 17:55:31 -0500
Subject: [PATCH 2/3] do not fail bq load if no files to ingest

---
 scripts/variantstore/wdl/ImportGenomes.wdl | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/scripts/variantstore/wdl/ImportGenomes.wdl b/scripts/variantstore/wdl/ImportGenomes.wdl
index fccfdc4552c..b8e5b41cbb5 100644
--- a/scripts/variantstore/wdl/ImportGenomes.wdl
+++ b/scripts/variantstore/wdl/ImportGenomes.wdl
@@ -322,15 +322,22 @@ task LoadTable {
     # even for non-superpartitioned tables (e.g. metadata), the TSVs do have the suffix
     FILES="~{datatype}_${PADDED_TABLE_ID}_*"
 
+    NUM_FILES=$(gsutil ls "${DIR}${FILES}" | wc -l)
+
     if [ ~{superpartitioned} = "true" ]; then
       TABLE="~{dataset_name}.${PREFIX}~{datatype}_${PADDED_TABLE_ID}"
     else
       TABLE="~{dataset_name}.${PREFIX}~{datatype}"
     fi
 
-    bq load --location=US --project_id=~{project_id} --skip_leading_rows=1 --source_format=CSV -F "\t" $TABLE $DIR$FILES ~{schema} || exit 1
-    echo "ingested ${FILES} file from $DIR into table $TABLE"
-    gsutil mv $DIR$FILES ${DIR}done/
+    if [ $NUM_FILES -gt 0 ]; then
+        bq load --location=US --project_id=~{project_id} --skip_leading_rows=1 --source_format=CSV -F "\t" $TABLE $DIR$FILES ~{schema} || exit 1
+        echo "ingested ${FILES} file from $DIR into table $TABLE"
+        gsutil mv $DIR$FILES ${DIR}done/
+    else
+        echo "no ${FILES} files to process in $DIR"
+    fi
+
   >>>
 
   runtime {

From 49f2c43a0a0db1b9dfa2378c08608ffc88756eb1 Mon Sep 17 00:00:00 2001
From: Morgan Taylor <marymorg@broadinstitute.org>
Date: Thu, 4 Mar 2021 10:41:30 -0500
Subject: [PATCH 3/3] remove feature branch from dockstore

---
 .dockstore.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.dockstore.yml b/.dockstore.yml
index 7ee538df647..0b9c4858a2b 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -57,7 +57,6 @@ workflows:
        branches:
          - master
          - ah_var_store
-         - mmt_reduce_mem
    - name: funcotator
      subclass: WDL
      primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl