Fixed incorrect number of outputs mentioned in error message in some …

…cases

Fixed referencing outputs[2] or greater failing
Made tolerant of a range of procs passed in config (procs="1-5") for resource managers that support that

src/main/groovy/bpipe/PipelineCategory.groovy

@@ -216,7 +216,7 @@ class PipelineCategory {
                             // If the filterInputs option is set, match input files on the region name
                             def childInputs = input
 
-                            def filterInputs = chr.config?.filterInputs
+                            def filterInputs = chr instanceof Chr ? chr.config?.filterInputs : "auto"
 
                             if(filterInputs == "auto") {
                                 filterInputs = Utils.box(input).any { it.matches(/.*\.chr[1-9A-Z_]*\..*$/) }
@@ -243,10 +243,10 @@ class PipelineCategory {
 
                             log.info "Adding dummy prior stage for thread ${Thread.currentThread().id} with outputs : $dummyPriorContext.output"
                             child.addStage(dummyPriorStage)
-                            def region = chr.region
+                            def region = chr instanceof Chr ? chr.region : ""
                             child.variables += [chr: region]
                             child.variables += [region: region]
-                            child.name = chr.name
+                            child.name = chr instanceof Chr ? chr.name : chr
                             child.runSegment(childInputs, segmentClosure)
                         }
                         catch(Exception e) {

src/main/groovy/bpipe/PipelineContext.groovy

@@ -405,7 +405,11 @@ class PipelineContext {
    }
 
    def getOutputs() {
-       return Utils.box(getOutput())
+       def raw =  getOutput()
+       // Used to 'box' the result, but now this is a PipelineOutput that supports direct access by index, 
+       // so should not need it
+//       def result =  Utils.box(raw)
+       return raw
    }
 
    def getOutputByIndex(int index) {
@@ -1408,8 +1412,13 @@ class PipelineContext {
       // which may get given a crazy high number of threads
       if(config) {
           def procs = command.getConfig(Utils.box(this.input)).procs
-          if(procs)
+          if(procs) {
+              if(procs instanceof String) {
+                 // Allow range of integers
+                 procs = procs.replaceAll(" *-.*\$","")
+              }
               actualThreads = String.valueOf(Math.min(procs.toInteger(), actualThreads.toInteger()))
+          }
       }
 
       command.command = joined.replaceAll(THREAD_LAZY_VALUE, actualThreads)

src/main/groovy/bpipe/PipelineOutput.groovy

@@ -119,10 +119,10 @@ class PipelineOutput {
      *   exec "cp foo.txt ${output[0]}"
      */
     String getAt(int i) {
-        def inputs = Utils.box(this.output)
-        if(inputs.size() <= i)
-            throw new PipelineError("Insufficient outputs:  output $i was referenced but there are only ${output.size()} outputs to choose from")
-        return inputs[i]
+        def outs = Utils.box(this.output)
+        if(outs.size() <= i)
+            throw new PipelineError("Insufficient outputs:  output ${i+1} was referenced but there are only ${outs.size()} outputs to choose from")
+        return outs[i]
     }
 
     /**

tests/custom_chr/run.sh

@@ -0,0 +1,9 @@
+source ../testsupport.sh
+
+run
+
+grep -q "^mars" test.out || err "Failed to find mars printed out"
+grep -q "^world" test.out || err "Failed to find world printed out"
+grep -q "^jupiter" test.out || err "Failed to find mars printed out"
+
+true

tests/custom_chr/test.groovy

@@ -0,0 +1,10 @@
+hello = {
+  exec "echo $branch"
+}
+
+parallel_paths = ["mars","world","jupiter"] as Set
+
+run {
+  parallel_paths * [ hello ]
+}
+

tests/multi_computed/$

@@ -0,0 +1 @@
+mars

tests/multi_computed/cleanup.sh

@@ -0,0 +1 @@
+rm -f e g  null out*.txt hello* 

tests/multi_computed/run.sh

@@ -0,0 +1,6 @@
+source ../testsupport.sh
+
+run 
+
+exists out1.txt out2.txt out3.txt
+

tests/multi_computed/test.groovy

@@ -0,0 +1,17 @@
+/* The example from the documentation */
+
+hello = {  
+        // Build a list of commands to execute in parallel
+        def outputs = (1..3).collect { "out${it}.txt" }
+
+        // Compute the commands we are going to execute
+	int n = 0
+        def commands =["mars","jupiter","earth"].collect{"echo $it > ${outputs[n++]}"} 
+
+        // Tell Bpipe to produce the outputs from the commands
+	produce(outputs) {
+	    multiExec commands
+	}
+}
+
+run { hello }