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Submission fixes 2

Ahmed Markhoos requested to merge submission-fixes-2 into master

Further fixes to the job submission and analyze.

List of bugs

  1. submission.py only uses the last job options in the config file. Thus, it is not possible to use different job options for different sampleFolder paths.
  2. submission.py does not submit the correct number of sub-samples. Resulting in an incomplete analyze sampleFolder.
  3. analyze.py breaks when an if-statement alias is called twice.

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