Move report options from command to config file

Author: Yan Xu

webapp/server/config.js

@@ -84,8 +84,10 @@ const config = {
     JOBS_INPUT_MAX_SIZE_BYTES: makeIntIfDefined(process.env.NEXTFLOW_JOBS_INPUT_MAX_SIZE_BYTES) || 161061273600,
     // Directory of the workflow files.
     WORKFLOW_DIR: process.env.NEXTFLOW_WORKFLOW_DIR || NEXTFLOW_BASE_DIR,
-    // Directory of the workflow templates. The Workflow templates are used for creating cromwell inputs.
+    // Directory of the workflow templates. The Workflow templates are used for creating nextflow workflow inputs.
     TEMPLATE_DIR: process.env.NEXTFLOW_TEMPLATE_DIR || path.join(NEXTFLOW_BASE_DIR, 'templates'),
+    // Directory of the workflow configs. The Workflow configs are used for running nextflow workflows.
+    CONFIG_DIR: process.env.NEXTFLOW_TEMPLATE_DIR || path.join(NEXTFLOW_BASE_DIR, 'configs'),
   },
   CROMWELL: {
     // Base URL at which HTTP clients can access the Cromwell API.

webapp/server/utils/nextflow.js

@@ -3,7 +3,7 @@ const fs = require('fs');
 const ejs = require('ejs');
 const Papa = require('papaparse');
 const Job = require('../edge-api/models/job');
-const { workflowList, generateWorkflowResult } = require('./workflow');
+const { nextflowConfigs, workflowList, generateWorkflowResult } = require('./workflow');
 const { write2log, execCmd, sleep } = require('./common');
 const logger = require('./logger');
 const config = require('../config');
@@ -13,7 +13,12 @@ const generateInputs = async (projHome, projectConf, proj) => {
   // workflowList in utils/workflow
   const workflowSettings = workflowList[projectConf.workflow.name];
   const template = String(fs.readFileSync(`${config.NEXTFLOW.TEMPLATE_DIR}/${workflowSettings.config_tmpl}`));
-  const params = { ...projectConf.workflow.input, outdir: `${projHome}/${workflowSettings.outdir}`, project: proj.name };
+  const params = {
+    ...projectConf.workflow.input,
+    outdir: `${projHome}/${workflowSettings.outdir}`,
+    project: proj.name,
+    report_config: `${config.NEXTFLOW.CONFIG_DIR}/${nextflowConfigs.report_config}`
+  };
   // render input template and write to nextflow_params.json
   const inputs = ejs.render(template, params);
   await fs.promises.writeFile(`${projHome}/nextflow.config`, inputs);
@@ -35,12 +40,8 @@ const submitWorkflow = async (proj, projectConf, inputsize) => {
     return;
   }
   // submit workflow
-  const runReport = `${projHome}/nextflow/report.html`;
-  const runTrace = `${projHome}/nextflow/trace.txt`;
-  const runTimeline = `${projHome}/nextflow/timeline.html`;
   const runName = `edge-${proj.code}`;
-  const nextflowRunOptions = `-with-report ${runReport} -with-trace ${runTrace} -with-timeline ${runTimeline}`;
-  const cmd = `cd ${workDir}; nextflow -c ${projHome}/nextflow.config -bg -q run ${config.NEXTFLOW.WORKFLOW_DIR}/${workflowList[projectConf.workflow.name].nextflow_main} -name ${runName} ${nextflowRunOptions}`;
+  const cmd = `cd ${workDir}; nextflow -c ${projHome}/nextflow.config -bg -q run ${config.NEXTFLOW.WORKFLOW_DIR}/${workflowList[projectConf.workflow.name].nextflow_main} -name ${runName}`;
   write2log(log, 'Run pipeline');
   // Don't need to wait for the command to complete. It may take long time to finish and cause an error.
   // The updateJobStatus will catch the error if this command failed.

webapp/server/utils/workflow.js

@@ -5,6 +5,9 @@ const config = require('../config');
 
 const cromwellWorkflows = ['sra2fastq'];
 const nextflowWorkflows = ['runFaQCs'];
+const nextflowConfigs = {
+  report_config: 'report.config',
+};
 
 const workflowList = {
   default_wdl_version: '1.0',
@@ -19,7 +22,7 @@ const workflowList = {
   },
   runFaQCs: {
     outdir: 'output/runFaQCs',
-    nextflow_main: 'testmain.nf',
+    nextflow_main: 'main.nf',
     config_tmpl: 'runFaQCs_config.tmpl',
   },
 };
@@ -84,6 +87,7 @@ const generateWorkflowResult = (proj) => {
 module.exports = {
   cromwellWorkflows,
   nextflowWorkflows,
+  nextflowConfigs,
   workflowList,
   linkUpload,
   generateWorkflowResult,

workflows/Nextflow/configs/report.config

@@ -0,0 +1,18 @@
+report {
+    enabled = true
+    file = 'report.html'
+    overwrite = true
+}
+
+timeline {
+    enabled = true
+    file = 'timeline.html'
+    overwrite = true
+}
+
+trace {
+    enabled = true
+    file = 'trace.txt'
+    fields = 'name,status,start,complete,duration'
+    overwrite = true
+}

workflows/Nextflow/templates/runFaQCs_config.tmpl

@@ -87,8 +87,4 @@ executor {
     submitRateLimit = '1/5sec'
 }
 
-trace {
-    enabled = true
-    file = 'trace.txt'
-    fields = 'name,status,start,complete,duration'
-}
+includeConfig "<%= report_config %>"