Refactored SPP plugin w/tellread support. (#92)

* Updated to support changes to submit_job.

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.

* Updated

* point to add_tellread branch of mg-scripts

* WIP: Refactored qp-klp plugin to support new pipelines

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.

* Update git w/latest on Workflows

* klp updated to use new classes, streamlined

* Added tests for Workflow creation using factory class.

Updated Assays and Instruments for Amplicon and TellSeq workflows.

* Reorganized sample input files into folders.

Reorganized sample input files into folders to allow for easier naming.

* Revamping existing tests

* Revamping NuQCJob tests

* New tests exercise ConvertJob and NuQCJob

* Updates from this week

* Updated Amplicon quality control test.

* Address test fail on MacOS vs Linux

* Updates

* Pre-test push

* Checkpoint

* checkpoint2

* Code audit

* All tests are passing again post metapool + mgscripts updates

* flake8

* smaller dummy files

* update test

* Updates

* Removed TODOs

* Updates

* Some updates based on feedback

* Removing .DS_Store

* Updates based on feedback

* Updates based on feedback

* Updates based on testing

* Updates based on feedback

Author: charles-cowart

.github/workflows/qiita-plugin-ci.yml

@@ -79,7 +79,8 @@ jobs:
           # seqtk is a conda-installed requirement for metapool and isn't
           # installed automatically by its setup.py.
           conda config --add channels bioconda
-          conda create -q --yes -n klp python=3.9 seqtk
+          conda create -q --yes -n klp python=3.9 'seqtk>=1.4'
+
           conda activate klp
 
           export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "pandas",
     "qiita-files@https://github.com/qiita-spots/qiita-files/archive/master.zip",
     "qiita_client@https://github.com/qiita-spots/qiita_client/archive/master.zip",
-    "sequence-processing-pipeline@https://github.com/biocore/mg-scripts/archive/master.zip",
+    "sequence-processing-pipeline@https://github.com/biocore/mg-scripts/archive/master.zip"
 ]
 [project.scripts]
 configure_klp = "qp_klp.scripts.configure_klp:config"