Add chunkprocessing via drmaa

psot/nextflow.py

@@ -17,8 +17,9 @@ def flatten(d, parent_key='', sep='_'):
 
 analysis_template = Template ('''
 process ${id} {
+    executor 'drmaa'
     input:
-    file fasta from for_${id}
+    file fasta from for_${id}.splitFasta(by:100, file:'input')
 
     output:
     file "$${fasta}.${id}.results" into ${id}_results
@@ -74,7 +75,7 @@ process convert_${id}_to_json {
     """
 }
 ''')
-input_template = Template('''    file ${id}_result from ${id}_json''')
+input_template = Template('''    file ${id}_result from ${id}_json.collect()''')
 join_jsons_template = Template('''
 process join_documents {