Make Nextflow compatible with NixOS (or other systems without /bin/bash)

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

@@ -65,6 +65,8 @@ class BashWrapperBuilder {
 
     static final public List<String> BASH
 
+    static final public List<String> ENV_BASH
+
     static private int level
 
     @PackageScope
@@ -85,6 +87,7 @@ class BashWrapperBuilder {
             log.warn "Invalid value for `NXF_DEBUG` variable: $str -- See http://www.nextflow.io/docs/latest/config.html#environment-variables"
         }
         BASH = Collections.unmodifiableList( level > 0 ? ['/bin/bash','-uex'] : ['/bin/bash','-ue'] )
+        ENV_BASH = Collections.unmodifiableList(['/usr/bin/env', '-S', 'bash', BASH[1]])
 
     }
 
@@ -571,7 +574,8 @@ class BashWrapperBuilder {
         final traceWrapper = isTraceRequired()
         if( traceWrapper ) {
             // executes the stub which in turn executes the target command
-            launcher = "/bin/bash ${fileStr(wrapperFile)} nxf_trace"
+            String traceInterpreter = runWithContainer ? "/bin/bash" : "/usr/bin/env bash"
+            launcher = "${traceInterpreter} ${fileStr(wrapperFile)} nxf_trace"
         }
         else {
             launcher = "${interpreter} ${fileStr(scriptFile)}"

modules/nextflow/src/main/groovy/nextflow/executor/local/LocalTaskHandler.groovy

@@ -131,7 +131,7 @@ class LocalTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     protected ProcessBuilder localProcessBuilder() {
-        final cmd = new ArrayList<String>(BashWrapperBuilder.BASH) << wrapperFile.getName()
+        final cmd = new ArrayList<String>(BashWrapperBuilder.ENV_BASH) << wrapperFile.getName()
         log.debug "Launch cmd line: ${cmd.join(' ')}"
         // make sure it's a posix file system
         if( task.workDir.fileSystem != FileSystems.default )

modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy

@@ -133,7 +133,7 @@ class TaskBean implements Serializable, Cloneable {
         this.condaEnv = task.getCondaEnv()
         this.spackEnv = task.getSpackEnv()
         this.moduleNames = task.config.getModule()
-        this.shell = task.config.getShell() ?: BashWrapperBuilder.BASH
+        this.shell = task.config.getShell(task.isContainerEnabled()) ?: BashWrapperBuilder.BASH
         this.script = task.getScript()
         this.beforeScript = task.config.getBeforeScript()
         this.afterScript = task.config.getAfterScript()

modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy

@@ -375,10 +375,10 @@ class TaskConfig extends LazyMap implements Cloneable {
         return (List<String>) get('secret')
     }
 
-    List<String> getShell() {
+    List<String> getShell(boolean isContainerEnabled = true) {
         final value = get('shell')
         if( !value )
-            return BashWrapperBuilder.BASH
+            return isContainerEnabled ? BashWrapperBuilder.BASH : BashWrapperBuilder.ENV_BASH
 
         if( value instanceof List )
             return (List)value

modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy

@@ -125,7 +125,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
     static final Map<String,Object> DEFAULT_CONFIG = [
             debug: false,
             cacheable: true,
-            shell: BashWrapperBuilder.BASH,
             maxRetries: 0,
             maxErrors: -1,
             errorStrategy: ErrorStrategy.TERMINATE
@@ -174,14 +173,15 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
      *
      * @param script The owner {@code BaseScript} configuration object
      */
-    protected ProcessConfig( BaseScript script ) {
+    protected ProcessConfig( BaseScript script, boolean isContainerEnabled = true) {
         ownerScript = script
         configProperties = new LinkedHashMap()
         configProperties.putAll( DEFAULT_CONFIG )
+        configProperties.put('shell', isContainerEnabled ? BashWrapperBuilder.BASH : BashWrapperBuilder.ENV_BASH)
     }
 
-    ProcessConfig( BaseScript script, String name ) {
-        this(script)
+    ProcessConfig( BaseScript script, String name, boolean isContainerEnabled = true) {
+        this(script, isContainerEnabled)
         this.processName = name
     }
 

modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy

@@ -100,7 +100,7 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         assert processConfig==null
 
         // the config object
-        processConfig = new ProcessConfig(owner,processName)
+        processConfig = new ProcessConfig(owner,processName,session.getContainerConfig().isEnabled())
 
         // Invoke the code block which will return the script closure to the executed.
         // As side effect will set all the property declarations in the 'taskConfig' object.