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CWL job chaining tests #3696

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Commits on Jul 2, 2021

  1. Prototype testing CWL job chaining for TOIL.

    The md_list_reduced*cwl workflows are added.
    md_list_reduced_2nests.cwl will chain 2 jobs,
    while for md_list_reduced.cwl (currently) no
    jobs are chained.
    
    The test uses the stats logfiles (so toilcwl
    must be run with --stats and --logDebug),
    pulling out the lists of CWL jobs which are
    run in each TOIL task.
    douglowe committed Jul 2, 2021
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Commits on Jul 4, 2021

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Commits on Jul 17, 2021

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Commits on Jul 22, 2021

  1. Pickle toilState to pass to workers for jobchaining work.

    The parent thread now pickle's toilState, passing
    it to the worker thread, where it is unpickled again.
    
    A test for completed predecessors for jobs with multiple
    predecessors has been added to the worker, so that some
    basic job chaining can be performed for jobs whose remaining
    predecessor completes within that task.
    
    This change does result in the parent thread not correctly
    noting jobs which had multiple predecessors have now been
    completed correctly. So some of the checks at the end of
    the internal job routine have had to be switched off for the
    moment.
    douglowe committed Jul 22, 2021
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Commits on Jul 26, 2021

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Commits on Aug 25, 2021

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  2. types and cleanups

    mr-c committed Aug 25, 2021
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Commits on Sep 21, 2021

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Commits on Sep 26, 2021

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Commits on Nov 17, 2021

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Commits on Nov 30, 2021

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Commits on Jan 31, 2022

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