Add possibility to set env variables for nextflow

src/main/html/webapp/components/admin/app/settings/settings.js

@@ -35,10 +35,13 @@ export default Control.extend({
     var nextflowProfile = $('#nextflow-profile').val();
     var nextflowConfig = $('#nextflow-config').val();
     var nextflowWork = $('#nextflow-work').val();
+    var nextflowEnv = $('#nextflow-env').val();
+
 
     this.application.attr('config').attr('nextflow.profile', nextflowProfile);
     this.application.attr('config').attr('nextflow.config', nextflowConfig);
     this.application.attr('config').attr('nextflow.work', nextflowWork);
+    this.application.attr('config').attr('nextflow.env', nextflowEnv);
     this.application.save(function (data) {
       bootbox.alert("Application settings updated.");
     },

src/main/html/webapp/components/admin/app/settings/settings.stache

@@ -14,16 +14,24 @@
   <input class="form-control" id="nextflow-work" name="nextflow-work" autocomplete="off" value="{{application.config.attr('nextflow.work')}}"/>
 
   <br><p>Custom Configuration:<br>
-  <small class="text-muted">All hardware specific parameters can be set here. If you use the AWSBatch profile this is the place to set your credentials</small></p>
+  <small class="text-muted">All app-specific parameters can be set here.</small></p>
 
 <div style=" display: flex;
    justify-content: center;
-   align-items: center;
+   align-items: flex-start;
    flex-direction: row;">
 
 <div style="    width: 75%; align-self: stretch;">
   <textarea class="form-control" id="nextflow-config" name="nextflow-config" style="height: 550px; font-size: 14px; font-family: SFMono-Regular, Menlo, Monaco, Consolas, Liberation Mono, Courier New, monospace;">{{application.config.attr('nextflow.config')}}</textarea>
 <br>
+
+<p>Custom Environment:<br>
+<small class="text-muted">All app-specific environment variables can be set here.</small></p>
+
+<textarea class="form-control" id="nextflow-env" name="nextflow-env" style="height: 550px; font-size: 14px; font-family: SFMono-Regular, Menlo, Monaco, Consolas, Liberation Mono, Courier New, monospace;">{{application.config.attr('nextflow.env')}}</textarea>
+
+<br>
+
 	<div class="form-group">
 		<button id="save" class="btn btn-primary" data-loading-text="please wait..."><i class="far fa-save"></i> Save changes</button>
 	</div>

src/main/java/cloudgene/mapred/jobs/Environment.java

@@ -40,6 +40,7 @@ public Environment addContext(CloudgeneContext context) {
 			add("JOB_PRIORITY", context.getJob().getPriority() + "");
 			add("JOB_SUBMITTED_ON", context.getJob().getSubmittedOn() + "");
 		}
+		add("JOB_LOCATION", context.getLocalTemp());
 		add("USER_NAME", context.getUser().getUsername());
 		add("USER_EMAIL", context.getUser().getMail());
 		add("USER_FULL_NAME", context.getUser().getFullName());

src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java

@@ -37,6 +37,8 @@ public class NextflowBinary {
 
 	private String name;
 
+	private File envScript;
+
 	public static NextflowBinary build(Settings settings) {
 		String binary = new BinaryFinder("nextflow").settings(settings, "nextflow", "home").env("NEXTFLOW_HOME")
 				.envPath().path("/usr/local/bin").find();
@@ -125,10 +127,17 @@ public void setName(String name) {
 		this.name = name;
 	}
 
+	public void setEnvScript(File envScript) {
+		this.envScript = envScript;
+	}
+
 	public List<String> buildCommand() {
 
 		List<String> nextflow = new Vector<String>();
 		nextflow.add("PATH=$PATH:/usr/local/bin");
+		if (envScript != null && envScript.exists()) {
+			nextflow.add("source " + envScript.getAbsolutePath() + ";");
+		}
 		nextflow.add(getBinary());
 
 		nextflow.add("-log");

src/main/java/cloudgene/mapred/plugins/nextflow/NextflowPlugin.java

@@ -21,6 +21,7 @@ public class NextflowPlugin implements IPlugin {
 	public static final String ID = "nextflow";
 	public static final String NEXTFLOW_CONFIG = "nextflow.config";
 	public static final String NEXTFLOW_YAML = "nextflow.yaml";
+	public static final String NEXTFLOW_ENV = "nextflow.env";
 
 	private Settings settings;
 
@@ -82,6 +83,10 @@ public void updateConfig(WdlApp app, Map<String, String> config) throws IOExcept
 		writer.write(properties);
 		writer.close();
 
+		String nextflowEnv = FileUtil.path(appFolder, NEXTFLOW_ENV);
+		String contentEnv = config.get("nextflow.env");
+		StringBuffer contentNextflowEnv = new StringBuffer(contentEnv == null ? "" : contentEnv);
+		FileUtil.writeStringBufferToFile(nextflowEnv, contentNextflowEnv);
 	}
 
 	@Override
@@ -114,6 +119,12 @@ public Map<String, String> getConfig(WdlApp app) throws IOException {
 			config.put("nextflow.work", properties.get("work").toString());
 		}
 
+		String nextflowEnv = FileUtil.path(appFolder, NEXTFLOW_ENV);
+		if (new File(nextflowEnv).exists()) {
+			String content = FileUtil.readFileAsString(nextflowEnv);
+			config.put("nextflow.env", content);
+		}
+
 		return config;
 
 	}

src/main/java/cloudgene/mapred/plugins/nextflow/NextflowStep.java

@@ -105,6 +105,10 @@ public boolean run(WdlStep step, CloudgeneContext context) {
 		String appConfig = FileUtil.path(appFolder, "nextflow.config");
 		nextflow.addConfig(appConfig);
 
+		String appEnv = FileUtil.path(appFolder, "nextflow.env");
+		nextflow.setEnvScript(new File(appEnv));
+
+
 		// set work directory
 		IWorkspace workspace = job.getWorkspace();