Refactored SPP plugin w/tellread support. #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.
Updated Assays and Instruments for Amplicon and TellSeq workflows.
Reorganized sample input files into folders to allow for easier naming.
charles-cowart
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Refactored SPP plugin to support TellSeq. Replaced Step() workflow class and its two children (Metagenomic, Amplicon) w/Mixins. The new base Workflow() class is mixed with an Assay class and a SequencingTech class to create a new subclass e.g. StandardMetagenomicWorkflow(). Metatranscriptomic was also implemented as a separate class as well. All workflows are now much more extensible.
Job submissions and tests also updated to support sacct -> squeue migration and to support multiple Slurm jobs in parallel and wait on 1+ jobs until they complete or terminate.