toil/wdl/wdl_synthesis.py

190         main_section = ''
194         main_section = main_section + main_header
198         main_section = main_section + jobs_to_write
203             main_section = main_section + main_destbucket
205         return main_section
222         main_section = ''
226         main_section = main_section + '        job0 = Job.wrapJobFn(initialize_jobs)\n'
233 … main_section += self.write_main_jobwrappers_declaration(self.workflows_dictionary[wf][assignment])
235                     main_section += '        job0 = job0.encapsulate()\n'
236 …        main_section += self.write_main_jobwrappers_call(self.workflows_dictionary[wf][assignment])
238                     main_section += '        job0 = job0.encapsulate()\n'
239 …     main_section += self.write_main_jobwrappers_scatter(self.workflows_dictionary[wf][assignment],
242 … main_section += '        if {}:\n'.format(self.workflows_dictionary[wf][assignment]['expression'])
243 …  main_section += self.write_main_jobwrappers_if(self.workflows_dictionary[wf][assignment]['body'])
245         main_section += '\n        fileStore.start(job0)\n'
247         return main_section
251         main_section = ''
260         main_section += '        {} = {}.create(\n                {})\n' \
265 …          main_section += '        {} = process_infile({}, fileStore)\n'.format(var_name, var_name)
267         return main_section
275         main_section = heredoc_wdl('''
284         return main_section
315         main_section = ''
318                 main_section += self.write_main_jobwrappers_declaration(if_statement[assignment])
320                 main_section += '        job0 = job0.encapsulate()\n'
321                 main_section += self.write_main_jobwrappers_call(if_statement[assignment])
323                 main_section += '        job0 = job0.encapsulate()\n'
324 …          main_section += self.write_main_jobwrappers_scatter(if_statement[assignment], assignment)
326                 main_section += '        if {}:\n'.format(if_statement[assignment]['expression'])
327                 main_section += self.write_main_jobwrappers_if(if_statement[assignment]['body'])
328         main_section = self.indent(main_section)
329         return main_section
334         main_section = '        {scatter} = job0.addChild({scatter}Cls('.format(scatter=assignment)
336             main_section += var + '=' + var + ', '
337         if main_section.endswith(', '):
338             main_section = main_section[:-2]
339         main_section += '))\n'
343 …main_section += '        {var} = {scatter}.rv("{var}")\n'.format(var=var['task'] + '_' + var['outp…
345         return main_section
409         main_section = '        {} = job0.addChild({}Cls('.format(task['alias'], task['task'])
411             main_section += var + '=' + task['io'][var] + ', '
412         if main_section.endswith(', '):
413             main_section = main_section[:-2]
414         main_section += '))\n'
418 …main_section += '        {var} = {task}.rv("{output}")\n'.format(var=var['task'] + '_' + var['outp…
421         return main_section
992                           main_section,  argument
1006             file.write(main_section)