readqc pipeline broken

[Acribbs]

I have encountered an error when running fastqc_screen. I see @AndreasHeger made some changes last week. Its stating that the outdir is missing from the dictionary (and it is). However, when I try to debug and specifically add outdir into the code it isn't being seen in the locals(). I have no idea why? - I will push the branch of my changes and see if you can see where I am going wrong.

I think the reason this bug has not been caught is that we no longer test FastqScreen as part of the pipeline_testing. now defaults as 0. Maybe we should change this? I think there may have been a specific reason why it was removed as a default, can you remember @sebastian-luna-valero

Thanks, Adam

Exception #40
      'builtins.KeyError("Error when creating command: could not find 'outdir' in dictionaries")' raised in ...
       Task = def pipeline_readqc.runFastqScreen(...):
       Job  = [i18-Carf-959_S4_L004.fastq.1.gz -> fastq_screen.dir/i18-Carf-959_S4_L004.fastqscreen]

    Traceback (most recent call last):
      File "/ifs/projects/adam/cgat-developers-v1/cgat-core/CGATCore/Pipeline/Execution.py", line 251, in interpolate_statement
        statement = statement % local_params
    KeyError: 'outdir'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ruffus/task.py", line 751, in run_pooled_job_without_exceptions
        register_cleanup, touch_files_only)
      File "/ifs/projects/adam/cgat-developers-v1/conda-install/envs/cgat-f/lib/python3.6/site-packages/ruffus/task.py", line 567, in job_wrapper_io_files
        ret_val = user_defined_work_func(*params)
      File "/ifs/projects/adam/cgat-developers-v1/cgat-flow/CGATPipelines/pipeline_readqc.py", line 469, in runFastqScreen
        P.run(statement, job_memory="8G")
      File "/ifs/projects/adam/cgat-developers-v1/cgat-core/CGATCore/Pipeline/Execution.py", line 1313, in run
        statement_list = [interpolate_statement(statement, options)]
      File "/ifs/projects/adam/cgat-developers-v1/cgat-core/CGATCore/Pipeline/Execution.py", line 255, in interpolate_statement
        "find %s in dictionaries" % msg)
    KeyError: "Error when creating command: could not find 'outdir' in dictionaries"

[Acribbs]

Branch is AC-fastq_screen

[Acribbs]

Have fixed issue with #28 . However, I think testing may need some thought because I dont think the fastq_screen is currently tested.