From ee915a43e405324e62ee5d4c14a6a6ec6c610058 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 24 Feb 2022 09:49:30 +0100
Subject: [PATCH] update svdb merge (#1274)

* update svdb merge

* fix undefined variable error

* remove prio join in the script block

* fix error

* fix error again

* update tests and refactor
---
 modules/svdb/merge/main.nf        | 12 ++++++++----
 tests/modules/svdb/merge/main.nf  | 10 ++++++++++
 tests/modules/svdb/merge/test.yml |  7 +++++++
 3 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
index 1f479ea4..505e2c0b 100644
--- a/modules/svdb/merge/main.nf
+++ b/modules/svdb/merge/main.nf
@@ -21,15 +21,19 @@ process SVDB_MERGE {
     script:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input  = ""
-    for (int index = 0; index < vcfs.size(); index++) {
-        input += " ${vcfs[index]}:${priority[index]}"
+    def input  = "${vcfs.join(" ")}"
+    def prio   = ""
+    if(priority) {
+        prio = "--priority ${priority.join(',')}"
+        for (int index = 0; index < vcfs.size(); index++) {
+            input += " ${vcfs[index]}:${priority[index]}"
+        }
     }
     """
     svdb \\
         --merge \\
         $args \\
-        --priority ${priority.join(',')} \\
+        $prio \\
         --vcf $input \\
         > ${prefix}_sv_merge.vcf
 
diff --git a/tests/modules/svdb/merge/main.nf b/tests/modules/svdb/merge/main.nf
index f417c3f7..3cbb4b44 100644
--- a/tests/modules/svdb/merge/main.nf
+++ b/tests/modules/svdb/merge/main.nf
@@ -14,3 +14,13 @@ workflow test_svdb_merge {
 
     SVDB_MERGE ( input, priority )
 }
+
+workflow test_svdb_merge_noprio {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    SVDB_MERGE ( input, [] )
+}
diff --git a/tests/modules/svdb/merge/test.yml b/tests/modules/svdb/merge/test.yml
index 8d16562f..46c4fef0 100644
--- a/tests/modules/svdb/merge/test.yml
+++ b/tests/modules/svdb/merge/test.yml
@@ -5,3 +5,10 @@
     - svdb/merge
   files:
     - path: output/svdb/test_sv_merge.vcf
+- name: svdb merge noprio
+  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf