Use shell directive with trace command in wrapper script

Signed-off-by: Ben Sherman <[email protected]>
nextflow-io · Sep 8, 2023 · 6e914aa · 6e914aa
1 parent 79c677a
commit 6e914aa
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Showing 5 changed files with 12 additions and 6 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -469,7 +469,7 @@ class BashWrapperBuilder {
         final traceWrapper = isTraceRequired()
         if( traceWrapper ) {
             // executes the stub which in turn executes the target command
-            launcher = "/bin/bash ${fileStr(wrapperFile)} nxf_trace"
+            launcher = "${shell.join(' ')} ${fileStr(wrapperFile)} nxf_trace"
         }
         else {
             launcher = "${interpreter} ${fileStr(scriptFile)}"

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -566,20 +566,25 @@ class BashWrapperBuilderTest extends Specification {
         when:
         binding = newBashWrapperBuilder(statsEnabled: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
         binding.unstage_controls == null
         binding.containsKey('unstage_controls')
 
         when:
         binding = newBashWrapperBuilder(statsEnabled: true, scratch: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
         binding.unstage_controls == '''\
                         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:
+        binding = newBashWrapperBuilder(statsEnabled: true, shell: ['/usr/local/bin/bash', '-ue']).makeBinding()
+        then:
+        binding.launch_cmd == '/usr/local/bin/bash -ue /work/dir/.command.run nxf_trace'
+
     }
 
     def 'should create launcher command with input' () {
@@ -1041,6 +1046,7 @@ class BashWrapperBuilderTest extends Specification {
         given:
         def bean = Mock(TaskBean) {
             inputFiles >> [:]
+            shell >> BashWrapperBuilder.BASH
         }
         def copy = Mock(ScriptFileCopyStrategy)
         bean.workDir >> Paths.get('/work/dir')

diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -281,7 +281,7 @@ on_term() {
 }
 
 nxf_launch() {
-    /bin/bash {{folder}}/.command.run nxf_trace
+    /bin/bash -ue {{folder}}/.command.run nxf_trace
 }
 
 nxf_stage() {

diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -235,7 +235,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
 
         binding.task_env == ''
 

diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
@@ -386,7 +386,7 @@ class AzFileCopyStrategyTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
 
         binding.task_env == '''\
                     export PATH="$PWD/.nextflow-bin:$AZ_BATCH_NODE_SHARED_DIR/bin/:$PATH"