From 54cd804811c7727597ae70a90eaeaddc6711e7a0 Mon Sep 17 00:00:00 2001
From: Yiming Yang <yang.yihming@gmail.com>
Date: Tue, 22 Sep 2020 23:48:06 -0400
Subject: [PATCH 1/2] Allow string type for calc_signature_scores

---
 workflows/cumulus/cumulus.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/cumulus/cumulus.wdl b/workflows/cumulus/cumulus.wdl
index 074dda8d..79a863bd 100644
--- a/workflows/cumulus/cumulus.wdl
+++ b/workflows/cumulus/cumulus.wdl
@@ -100,7 +100,7 @@ workflow cumulus {
 		# Random number generator seed. [default: 0]
 		Int? random_state
 		# Calculate signature scores for gene sets in <GMT_file>.
-		File? calc_signature_scores
+		String? calc_signature_scores
 		# Number of PCs. [default: 50]
 		Int? nPC
 		# Number of neighbors used for constructing affinity matrix. [default: 100]

From d34ae03f7dbcd1cd377dabc225377223e9cec524 Mon Sep 17 00:00:00 2001
From: Yiming Yang <yang.yihming@gmail.com>
Date: Wed, 23 Sep 2020 15:40:22 -0400
Subject: [PATCH 2/2] update calc_signature_scores input

---
 workflows/cumulus/cumulus.wdl       |  4 ++--
 workflows/cumulus/cumulus_tasks.wdl | 15 ++++++++++++---
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/workflows/cumulus/cumulus.wdl b/workflows/cumulus/cumulus.wdl
index 79a863bd..11f1371b 100644
--- a/workflows/cumulus/cumulus.wdl
+++ b/workflows/cumulus/cumulus.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "https://api.firecloud.org/ga4gh/v1/tools/cumulus:cumulus_tasks/versions/22/plain-WDL/descriptor" as tasks
+import "https://api.firecloud.org/ga4gh/v1/tools/cumulus:cumulus_tasks/versions/23/plain-WDL/descriptor" as tasks
 # import "cumulus_tasks.wdl" as tasks
 
 workflow cumulus {
@@ -302,7 +302,7 @@ workflow cumulus {
 			correction_method = correction_method,
 			batch_group_by = batch_group_by,
 			random_state = random_state,
-			gene_signature_file = calc_signature_scores,
+			gene_signature_set = calc_signature_scores,
 			nPC = nPC,
 			knn_K = knn_K,
 			knn_full_speed = knn_full_speed,
diff --git a/workflows/cumulus/cumulus_tasks.wdl b/workflows/cumulus/cumulus_tasks.wdl
index 47329909..87795156 100644
--- a/workflows/cumulus/cumulus_tasks.wdl
+++ b/workflows/cumulus/cumulus_tasks.wdl
@@ -108,7 +108,7 @@ task run_cumulus_cluster {
 		String? correction_method
 		String? batch_group_by
 		Int? random_state
-		File? gene_signature_file
+		String? gene_signature_set
 		Int? nPC
 		Int? knn_K
 		Boolean? knn_full_speed
@@ -151,11 +151,17 @@ task run_cumulus_cluster {
 		String docker_registry
 	}
 
+	Boolean is_url = defined(gene_signature_set) && sub(select_first([gene_signature_set]), "^gs://.+", "URL") == "URL"
+
 	command {
 		set -e
 		export TMPDIR=/tmp
 		monitor_script.sh > monitoring.log &
 
+		if [ ~{is_url} == true ]; then
+			gsutil -q cp ~{gene_signature_set} gene_signature.gmt
+		fi
+
 		python <<CODE
 		from subprocess import check_call
 
@@ -210,8 +216,11 @@ task run_cumulus_cluster {
 			call_args.extend(['--counts-per-cell-after', '~{counts_per_cell_after}'])
 		if '~{random_state}' is not '':
 			call_args.extend(['--random-state', '~{random_state}'])
-		if '~{gene_signature_file}' is not '':
-			call_args.extend(['--calc-signature-scores', '~{gene_signature_file}'])
+		if '~{gene_signature_set}' is not '':
+			if '~{is_url}' is 'true':
+				call_args.extend(['--calc-signature-scores', 'gene_signature.gmt'])
+			else:
+				call_args.extend(['--calc-signature-scores', '~{gene_signature_set}'])
 		if '~{no_select_hvf}' is 'true':
 			call_args.append('--no-select-hvf')
 		if '~{select_hvf_flavor}' is not '':