biocore / mg-scripts / 12146228444

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Add tellread (#149)

* initial add

* initial cleanup

* first pass at converting TELLREAD scripts

* Second pass at integrating tellread scripts

* third pass adding tellread

* fourth pass

* Fifth pass, tested on qiita-rc and then refactored.

* Manually merged with current master

* Manually merged with master

* Updates based on testing in qiita-rc

* flake8

* Small fixes

* Refactor KISSLoader to be more DRY.

* Pipeline.py updated to support changes in qp-klp

* Version 2.0 of TellSeq support.

Version 2.0 of TellSeq support removes the master tellread.sh script and
the drop-in replacement TRConvertJob.py for Job()s that wrap individual
steps in the original script. These steps can be used in whole or in
part in varying order in the refactored SPP plugin (qp-klp).

* Creation tests added for new TellReadJob() class.

* flake8

* New sample files added

* Added optional parameter to Pipeline() class.

Added optional parameter to Pipeline() class that overwrites the values in the lane column of a sample-sheet's data section.
This functionality used to reside in the qp-klp plugin and is a common usage pattern.
This allows SPP to override the value in a sample-sheet's lane column with the value provided by the user at submission time.

* bugfix

* Fixes error

Fixes error found when post-processing adapter-trimmed fastq files.
All files were being moved into one of the project sub-folders, rather than into their associated folders.
This appears to be due to recent implementation change.
All files are now moved into their correct folder.

* Rewrote test

* Updated branch to use new DFSheet() functionality

* Updated to recent changes in metapool

* Update from testing

* Updates to TRIntegrateJob based on testing

* Updated sample config file

* Replaced legacy exit check for tellread

* recent updates

* Updated tests

* Update setup.py to point to merged metapool updates
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