Add nextflow path

Author: Yan Xu

webapp/server/.env.example

@@ -38,3 +38,6 @@ SEND_PROJECT_STATUS_EMAILS=false
 PROJECT_STATUS_SUBJECT=Your EDGE project status
 EMAIL_MAILGUN_API_KEY="__POPULATE_ME_IF_ENABLING_EMAIL__"
 EMAIL_MAILGUN_DOMAIN="__POPULATE_ME_IF_ENABLING_EMAIL__"
+
+# Nextflow
+NEXTFLOW_PATH="/PATH/TO/nextflow"

webapp/server/config.js

@@ -77,6 +77,7 @@ const config = {
     BUILD_DIR: process.env.CLIENT_BASE_DIR || path.join(CLIENT_BASE_DIR, 'build'),
   },
   NEXTFLOW: {
+    PATH: process.env.NEXTFLOW_PATH || 'nextflow',
     // Max allowed number of jobs in nextflow.
     NUM_JOBS_MAX: makeIntIfDefined(process.env.NEXTFLOW_NUM_JOBS_MAX) || 100000,
     // Total size of the input files allowed per job.

webapp/server/utils/nextflow.js

@@ -44,7 +44,7 @@ const submitWorkflow = async (proj, projectConf, inputsize) => {
   }
   // submit workflow
   const runName = `edge-${proj.code}`;
-  const cmd = `cd ${workDir}; nextflow -c ${projHome}/nextflow.config -bg -q run ${config.NEXTFLOW.WORKFLOW_DIR}/${workflowList[projectConf.workflow.name].nextflow_main} -name ${runName}`;
+  const cmd = `cd ${workDir}; ${config.NEXTFLOW.PATH} -c ${projHome}/nextflow.config -bg -q run ${config.NEXTFLOW.WORKFLOW_DIR}/${workflowList[projectConf.workflow.name].nextflow_main} -name ${runName}`;
   write2log(log, 'Run pipeline');
   // Don't need to wait for the command to complete. It may take long time to finish and cause an error.
   // The updateJobStatus will catch the error if this command failed.
@@ -148,7 +148,7 @@ const updateJobStatus = async (job, proj) => {
   // get job status
   const projHome = `${config.IO.PROJECT_BASE_DIR}/${proj.code}`;
   // Pipeline status. Possible values are: OK, ERR and empty
-  let cmd = `cd ${projHome}/nextflow; nextflow log|awk '/${job.id}/ &&(/OK/||/ERR/)'|awk '{split($0,array,/\t/); print array[4]}'`;
+  let cmd = `cd ${projHome}/nextflow; ${config.NEXTFLOW.PATH} log|awk '/${job.id}/ &&(/OK/||/ERR/)'|awk '{split($0,array,/\t/); print array[4]}'`;
   let ret = await execCmd(cmd);
 
   if (!ret || ret.code !== 0) {
@@ -177,7 +177,7 @@ const updateJobStatus = async (job, proj) => {
   }
 
   // Task status. Possible values are: COMPLETED, FAILED, and ABORTED.
-  cmd = `cd ${projHome}/nextflow; nextflow log ${job.id} -f status`;
+  cmd = `cd ${projHome}/nextflow; ${config.NEXTFLOW.PATH} log ${job.id} -f status`;
   ret = await execCmd(cmd);
   if (!ret || ret.code !== 0) {
     // command failed