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

@@ -21,15 +21,19 @@ process SVDB_MERGE {
     script:
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input  = ""
+    def input  = "${vcfs.join(" ")}"
-    for (int index = 0; index < vcfs.size(); index++) {
+    def prio   = ""
-        input += " ${vcfs[index]}:${priority[index]}"
+    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
 

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, [] )
+}

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