fix wrong output selected from produce when suffix matches

Author: ssadedin

src/main/groovy/bpipe/SelectFromPredefinedFileNameMapper.groovy

@@ -27,7 +27,10 @@ class SelectFromPredefinedFileNameMapper implements FileNameMapper {
 
         final String name = segments[-1]
         final String dotName = '.' + name
-        final endExt = segments.join('.')
+        
+        // note: without the leading dot, can result in incorrect substring matches,
+        // eg: .gvcf matches .vcf
+        final endExt = '.' + segments.join('.')
 
         String result = this.overrideOutputs.find { 
             String.valueOf(it).endsWith(endExt) 

tests/multiext/cleanup.sh

@@ -0,0 +1 @@
+rm -f *.world.* foo.gvcf.gz foo.vcf.gz

tests/multiext/run.sh

@@ -0,0 +1,9 @@
+source ../testsupport.sh
+
+run
+
+grep -q 'foo.vcf.gz .* foo.vcf.world.txt' test.out || err "Selected wrong output from produce when only partial suffix matches"
+
+exists foo.vcf.world.txt
+
+

tests/multiext/test.groovy

@@ -0,0 +1,20 @@
+
+
+hello = {
+    produce('foo.gvcf.gz', 'foo.vcf.gz') {
+        exec """
+            touch $output.gvcf.gz $output.vcf.gz
+        """
+    }
+}
+
+world = {
+    exec """
+        cp -v $input.vcf.gz $output.txt
+    """
+}
+
+run {
+    hello + world
+}
+