cgat-developers/cgat-core

tmpdir missing parameter accessed

Closed this issue · 1 comments

I have a small ruffus pipeline that was previously ran without the need for a configuration file. However, when I try to run it using the new CGAT core it complains with the following error:

Traceback (most recent call last):
  File "convert_fastq.py", line 32, in <module>
    sys.exit(P.main(sys.argv))
  File "/ifs/projects/adam/cgat-developers-v2/cgat-core/CGATCore/Pipeline/Control.py", line 1318, in main
    run_workflow(options, args)
  File "/ifs/projects/adam/cgat-developers-v2/cgat-core/CGATCore/Pipeline/Control.py", line 1071, in run_workflow
    if not os.path.exists(get_params()["tmpdir"]):
  File "/ifs/projects/adam/cgat-developers-v2/cgat-core/CGATCore/Pipeline/Parameters.py", line 51, in __call__
    raise KeyError("missing parameter accessed")
KeyError: 'missing parameter accessed'

It seems as though I require a pipeline.yml with the tmpdir set. I thought that the tmpdir is set as a default in the main default configuration? Does this mean that I dont have my environment correctly configured or I now require this to be set in a configuration file?

Sorry I know why this isnt working now. It seems as though you always have to have the get_parameters function imported as standard.