Fix stage script in Fusion script launcher (#4109)

Signed-off-by: Ben Sherman <[email protected]>
nextflow-io · Jul 19, 2023 · 0933f47 · 0933f47
1 parent d39866e
commit 0933f47
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 0 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
@@ -110,6 +110,11 @@ class FusionScriptLauncher extends BashWrapperBuilder {
         return remoteWorkDir.resolve(TaskRun.CMD_INFILE)
     }
 
+    @Override
+    protected Path targetStageFile() {
+        return remoteWorkDir.resolve(TaskRun.CMD_STAGE)
+    }
+
     List<String> fusionSubmitCli(TaskRun task) {
         final runFile = toContainerMount(task.workDir.resolve(TaskRun.CMD_RUN), scheme)
         return List.of(FUSION_PATH, 'bash', runFile.toString())

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -165,6 +165,7 @@ class BashWrapperBuilderTest extends Specification {
         builder.targetInputFile() == folder.resolve('.command.in')
         builder.targetScriptFile() == folder.resolve('.command.sh')
         builder.targetWrapperFile() == folder.resolve('.command.run')
+        builder.targetStageFile() == folder.resolve('.command.stage')
         and:
         Files.exists(folder.resolve('.command.sh'))
         Files.exists(folder.resolve('.command.run'))