WIP: Updated to support changes to submit_job. #92
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Updated to support recent changes to Job.submit_job(). These changes allow for submitting multiple Slurm jobs in parallel and waiting on 1+ jobs until they complete or terminate. Added basic support for TellRead.
Refactored qp-klp plugin using mixins to break up tellseq.sh into components and support a version 2.0 Tellread workflow in mg-scripts. klp.py needs more cleanup and the tests need to be refactored. All references to Step in klp need to be replaced. The actual execute_pipeline() function for TellSeq Workflow() needs to be pasted from StandardMetagenomicWorkflow() and modified to use the new TellReadJob() class in mg-scripts.
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Updated to support recent changes to Job.submit_job(). These changes allow for submitting multiple Slurm jobs in parallel and waiting on 1+ jobs until they complete or terminate.
Added basic support for TellRead.
Refactored qp-klp plugin. Replaced the basic Step workflow class and its two children Metagenomic and Amplicon w/Mixins. The new base Workflow() class can be mixed with an Assay class and Instrument class to create a new subclass e.g. StandardMetagenomicWorkflow(). The new TellReadMetagenomicWorkflow will retain the Metagenomic assay class, but substitute a TellSeq instrument for the Illumina instrument.
tests still need to be refactored and a little bit of cleanup is left. Some recent changes to mg-scripts are also in progress.