Fix shell directive with trace command in wrapper script (#4292)

Signed-off-by: Ben Sherman <bentshermann@gmail.com> Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Jan 17, 2025 · 8342889 · 8342889
1 parent 7439ce2
commit 8342889
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Showing 2 changed files with 42 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
@@ -563,6 +563,14 @@ class BashWrapperBuilder {
         statsEnabled || fixOwnership()
     }
 
+    protected String shellPath() {
+        // keep the shell path as "/bin/bash" when a non-custom "shell" attribute is specified
+        // to not introduce unexpected changes due to the fact BASH is defined as "/bin/bash -eu" by default
+        return shell.is(BASH)
+            ? "/bin/bash"
+            : shell.join(' ')
+    }
+
     protected String getLaunchCommand(String interpreter, String env) {
         /*
         * process stats
@@ -574,7 +582,7 @@ class BashWrapperBuilder {
         final traceWrapper = isTraceRequired()
         if( traceWrapper ) {
             // executes the stub which in turn executes the target command
-            launcher = "/bin/bash ${fileStr(wrapperFile)} nxf_trace"
+            launcher = "${shellPath()} ${fileStr(wrapperFile)} nxf_trace"
         }
         else {
             launcher = "${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
@@ -688,6 +688,38 @@ class BashWrapperBuilderTest extends Specification {
 
     }
 
+    def 'should enable trace feature with custom shell' () {
+        when:
+        def binding = newBashWrapperBuilder(statsEnabled: false, shell: ['/bin/bash', '-ue']).makeBinding()
+        then:
+        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.sh'
+        binding.unstage_controls == null
+        binding.containsKey('unstage_controls')
+
+        when:
+        binding = newBashWrapperBuilder(statsEnabled: true, shell: ['/bin/bash', '-eu']).makeBinding()
+        then:
+        binding.launch_cmd == '/bin/bash -eu /work/dir/.command.run nxf_trace'
+        binding.unstage_controls == null
+        binding.containsKey('unstage_controls')
+
+        when:
+        binding = newBashWrapperBuilder(statsEnabled: true, scratch: true, shell: ['/bin/bash', '-eu']).makeBinding()
+        then:
+        binding.launch_cmd == '/bin/bash -eu /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' () {
 
         when:
@@ -1192,6 +1224,7 @@ class BashWrapperBuilderTest extends Specification {
         given:
         def bean = Mock(TaskBean) {
             inputFiles >> [:]
+            shell >> BashWrapperBuilder.BASH
             outputFiles >> []
         }
         def copy = Mock(ScriptFileCopyStrategy)