Improve api to enable wr executor

Merges #1148
nextflow-io · Jan 20, 2020 · 21088ad · 21088ad
1 parent 87cdddc
commit 21088ad
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -133,6 +133,10 @@ class BashWrapperBuilder {
         return "NXF_SCRATCH=\"\$(set +u; nxf_mktemp $scratchStr)\""
     }
 
+    protected boolean shouldUnstageOutputs() {
+        return workDir != targetDir
+    }
+
     protected boolean fixOwnership() {
         systemOsName == 'Linux' && containerConfig?.fixOwnership && runWithContainer && containerConfig.engine == 'docker' // <-- note: only for docker (shifter is not affected)
     }
@@ -256,7 +260,7 @@ class BashWrapperBuilder {
         binding.unstage_cmd = getUnstageCommand()
         binding.unstage_controls = changeDir ? getUnstageControls() : null
 
-        if( changeDir || workDir != targetDir ) {
+        if( changeDir || shouldUnstageOutputs() ) {
             binding.unstage_outputs = copyStrategy.getUnstageOutputFilesScript(outputFiles,targetDir)
         }
         else {

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -654,5 +654,13 @@ class TaskPollingMonitor implements TaskMonitor {
             log.debug "Failed to kill pending tasks ${batch} -- cause: ${e.message}"
         }
     }
+
+    /**
+     * The queue of tasks pending for submission to the underlying execution system
+     */
+    protected Queue<TaskHandler> getPendingQueue() {
+        return pendingQueue
+    }
+
 }