Fix missing .command.env when eval is used and task runs on a cloud e…

…nv [ci fast] Signed-off-by: Thanh Lee <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Sep 3, 2024 · 4a6b54a · 4a6b54a
1 parent 4667241
commit 4a6b54a
Show file tree

Hide file tree

Showing 2 changed files with 41 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
@@ -757,7 +757,7 @@ class BashWrapperBuilder {
         result += copyFileToWorkDir(TaskRun.CMD_ERRFILE) + ' || true' + ENDL
         if( statsEnabled )
             result += copyFileToWorkDir(TaskRun.CMD_TRACE) + ' || true' + ENDL
-        if(  outputEnvNames )
+        if( outputEnvNames || outputEvals )
             result += copyFileToWorkDir(TaskRun.CMD_ENV) + ' || true' + ENDL
         return result
     }

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -1320,6 +1320,46 @@ class BashWrapperBuilderTest extends Specification {
 
     }
 
+    def 'should get unstage control script'(){
+        given:
+        BashWrapperBuilder builder
+        when:
+        builder = newBashWrapperBuilder()
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                '''.stripIndent()
+
+
+        when:
+        builder = newBashWrapperBuilder(statsEnabled: true)
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.trace /work/dir/.command.trace || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEnvNames: ['some-data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEvals: [some:'data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+    }
+
 
     def 'should create wrapper with podman' () {
         when: