fix inputs passed in wrong order to parallel stage after 'produce' wh…

…en lexical sorting differs to input order

src/main/groovy/bpipe/InputSplitter.groovy

@@ -1,9 +1,12 @@
 package bpipe
 
 import groovy.util.logging.Log;
+
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import javax.naming.ldap.SortResponseControl;
+
 /**
  * Implements logic for splitting input files into groups by sample using simple
  * wildcard patterns.  The goal is to provide a simpler way for people to specify
@@ -26,6 +29,8 @@ import java.util.regex.Pattern;
  */
 @Log
 class InputSplitter {
+
+	boolean sortResults = true
 
     /**
      * Splits the given inputs up according to the specified pattern 
@@ -85,11 +90,17 @@ class InputSplitter {
             unsortedResult[group] << inp
 		}
 
-		// We now have all the inputs keyed on the part matching the split char, 
-		// however we want to also sort them 
-        Map sortedResult = [:]
-        unsortedResult.each {  k,v ->
-            sortedResult[k] = this.sortNumericThenLexically(pattern, splitGroups, v)
+		if(sortResults) {
+			// We now have all the inputs keyed on the part matching the split char, 
+			// however we want to also sort them 
+	        Map sortedResult = [:]
+	        unsortedResult.each {  k,v ->
+	            sortedResult[k] = this.sortNumericThenLexically(pattern, splitGroups, v)
+			}
+			return sortedResult
+		}
+		else {
+			return unsortedResult
 		}
     }
 

src/main/groovy/bpipe/PipelineCategory.groovy

@@ -156,7 +156,7 @@ class PipelineCategory {
      */
     static Object plus(Closure other, List segments) {
         Pipeline pipeline = Pipeline.currentUnderConstructionPipeline
-        Closure mul = splitOnFiles("*", segments, false)
+        Closure mul = splitOnFiles("*", segments, false, false)
         def plusImplementation =  { input1 ->
 
             def currentStage = new PipelineStage(Pipeline.currentRuntimePipeline.get().createContext(), other)
@@ -331,15 +331,15 @@ class PipelineCategory {
      * @param requireMatch  if true, the pipeline will fail if there are 
      *                      no matches to the pattern
      */
-    static Object splitOnFiles(def pattern, List segments, boolean requireMatch) {
+    static Object splitOnFiles(def pattern, List segments, boolean requireMatch, boolean sortResults=true) {
         Pipeline pipeline = Pipeline.currentRuntimePipeline.get() ?: Pipeline.currentUnderConstructionPipeline
 
         def multiplyImplementation = { input ->
 
             log.info "multiply on input $input with pattern $pattern"
 
             // Match the input
-            InputSplitter splitter = new InputSplitter()
+            InputSplitter splitter = new InputSplitter(sortResults:sortResults)
             Map samples = splitter.split(pattern, input)
 
             if(samples.isEmpty() && !requireMatch && pattern == "*")        

src/main/groovy/bpipe/PipelineContext.groovy

@@ -959,7 +959,7 @@ class PipelineContext {
 
         if(doExecute) {
             if(Utils.box(this.@output)) {
-                this.output = Utils.box(fixedOutputs) +  Utils.box(this.@output)
+                this.output = Utils.box(fixedOutputs) +  Utils.box(this.@output).grep { ! it in fixedOutputs }
                 this.output.removeAll { it in replacedOutputs  || toOutputFolder(it) in replacedOutputs}
             }
             else {

tests/ordered_input_to_parallel/cleanup.sh

@@ -0,0 +1 @@
+rm -f *cutadapt.*

tests/ordered_input_to_parallel/run.sh

@@ -0,0 +1,7 @@
+source ../testsupport.sh
+
+run 
+
+grep -q "inputs should not be equal" test.out && err "Input referenced multiple times"
+
+true

tests/ordered_input_to_parallel/test.groovy

@@ -0,0 +1,13 @@
+
+cutadapt = {
+    produce(["cutadapt.1.fq.gz", "cutadapt.2.fq.gz"]){
+         exec "touch $output1; touch $output2; " 
+    }
+}
+
+tophat = {
+      if(input1.toString() == input2.toString())
+          fail "inputs should not be equal"
+}
+
+run { cutadapt + [tophat] }