Replace drmaa with SGE

psot/nextflow.py

@@ -18,6 +18,7 @@ def flatten(d, parent_key='', sep='_'):
 analysis_template = Template ('''
 process ${id} {
     executor '${executor}'
+    ${clusterOptions}
     input:
     file fasta from for_${id}${chunks}
 
@@ -127,8 +128,6 @@ def setup_execution_directory(execution):
 
 def execute_analysis(execution):
     old_cwd = os.getcwd()
-    if execution['use_cluster']:
-        os.environ['NXF_DRMAA'] = '/usr/share/java/drmaa.jar'
     os.chdir(execution['directory'])
     os.system('nextflow run ' + execution['directory'] + '/main.nf --fasta ' + execution['fasta'] + ' --output ' + execution['output'])
     os.chdir(old_cwd)
@@ -145,11 +144,13 @@ Channel.fromPath(params.fasta).set{fasta}''')
     for m in modules:
         config = flatten(m)
         if execution['use_cluster']:
-            config['executor'] = 'drmaa'
+            config['executor'] = 'sge'
             config['chunks'] = ".splitFasta(by:300, file:'input')"
+            config['clusterOptions'] = "clusterOptions='-S /bin/bash'"
         else:
             config['executor'] = 'local'
             config['chunks'] = ''
+            config['clusterOptions'] = ''
 
         fragments.append(analysis_template.substitute(config))
         if execution['mode'] == 'live':