Fix unstage controls in command.run when using storeDir (#6364)

Signed-off-by: jorgee <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>

Author: jorgee

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -160,6 +160,18 @@ class BashWrapperBuilder {
         return targetDir && workDir!=targetDir
     }
 
+    /**
+     * Template method that allows controlling if it's required to unstage
+     * task control files (.command.out, .command.err, .command.trace, .command.env)
+     *
+     * See also https://github.com/nextflow-io/nextflow/pull/6364
+     * 
+     * @return false by default; executors may override to implement their own logic
+     */
+    protected boolean shouldUnstageControls() {
+        return false
+    }
+
     protected boolean fixOwnership() {
         // note: only for docker (other container runtimes are not affected)
         ContainerHelper.fixOwnership(containerConfig) && isLinuxOS() && runWithContainer
@@ -379,7 +391,7 @@ class BashWrapperBuilder {
         binding.launch_cmd = getLaunchCommand(interpreter,env)
         binding.stage_cmd = getStageCommand()
         binding.unstage_cmd = getUnstageCommand()
-        binding.unstage_controls = changeDir || shouldUnstageOutputs() ? getUnstageControls() : null
+        binding.unstage_controls = changeDir || shouldUnstageControls() ? getUnstageControls() : null
 
         if( changeDir || shouldUnstageOutputs() ) {
             binding.unstage_outputs = copyStrategy.getUnstageOutputFilesScript(outputFiles,targetDir)

plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchScriptLauncher.groovy

@@ -33,4 +33,9 @@ class AzBatchScriptLauncher extends BashWrapperBuilder {
     protected boolean shouldUnstageOutputs() {
         return true
     }
+
+    @Override
+    protected boolean shouldUnstageControls() {
+        return true
+    }
 }

tests/checks/unstage-controls-storedir.nf/.checks

@@ -0,0 +1,14 @@
+set -e
+
+#
+# run normal mode and check if execution has unnecesary trying to copy .command.out and .command.err in the same directory. 
+# https://github.com/nextflow-io/nextflow/issues/6311
+#
+echo ''
+rm -rf work/* || true 
+NXF_WORK=work $NXF_RUN
+
+if grep -qR  "are the same file" work/ ; then
+	echo "ERROR: Unnecessary copy of controls"
+	exit 1
+fi

tests/unstage-controls-storedir.nf

@@ -0,0 +1,17 @@
+// Test to validate unstage controls copy error is not printed whe using storeDir. https://github.com/nextflow-io/nextflow/issues/6311
+
+workflow {
+  test()
+}
+
+process test {
+    storeDir "test"
+
+    output:
+    path "test.txt"
+
+    script:
+    """
+    ls > test.txt
+    """
+}