`debugWorkflow`¶

Module Contents¶

`initialize_jobs`(job)	Stub function used to start a toil workflow since toil workflows can only
`writeA`(job, mkFile)	Runs a program, and writes a string 'A' into A.txt using mkFile.py.
`writeB`(job, mkFile, B_file)	Runs a program, extracts a string 'B' from an existing file, B_file.txt, and
`writeC`(job)	Creates/writes a file, C.txt, containing the string 'C'.
`writeABC`(job, A_dict, B_dict, C_dict, filepath)	Takes 3 files (specified as dictionaries) and writes their contents to ABC.txt.
`finalize_jobs`(job, num)	Does nothing but should be recorded in stats, status, and printDot().
`broken_job`(job, num)	A job that will always fail. To be used for a tutorial.

`logger`	This workflow's purpose is to create files and jobs for viewing using stats,
`jobStorePath`

debugWorkflow.logger¶: This workflow’s purpose is to create files and jobs for viewing using stats, status, and printDot() in toilDebugTest.py. It’s intended for future use in a debugging tutorial containing a broken job. It is also a minor integration test.

debugWorkflow.initialize_jobs(job)¶: Stub function used to start a toil workflow since toil workflows can only start with one job (but afterwards can run many in parallel).

debugWorkflow.writeA(job, mkFile)¶: Runs a program, and writes a string ‘A’ into A.txt using mkFile.py.

debugWorkflow.writeB(job, mkFile, B_file)¶: Runs a program, extracts a string ‘B’ from an existing file, B_file.txt, and writes it into B.txt using mkFile.py.

debugWorkflow.writeC(job)¶: Creates/writes a file, C.txt, containing the string ‘C’.

debugWorkflow.writeABC(job, A_dict, B_dict, C_dict, filepath)¶: Takes 3 files (specified as dictionaries) and writes their contents to ABC.txt.

debugWorkflow.finalize_jobs(job, num)¶: Does nothing but should be recorded in stats, status, and printDot().

debugWorkflow.broken_job(job, num)¶: A job that will always fail. To be used for a tutorial.