Added support for replicates. Test needed.

charles-cowart commented 1 year ago

This is how GenPrepFileJob will use the new functionality in metapool to transparently handle replicates. The code is here but I need to write a good test.

charles-cowart commented 1 year ago

This PR depends on an update to metapool (https://github.com/biocore/metagenomics_pooling_notebook/pull/134). 134 is currently failing due to a Qiita dependency. This issue will be looked into shortly.

coveralls commented 1 year ago

Pull Request Test Coverage Report for Build 5618669683

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

64 of 69 (92.75%) changed or added relevant lines in 2 files are covered.
5 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.3%) to 83.22%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
sequence_processing_pipeline/GenPrepFileJob.py	34	39	87.18%
<!--	Total:	64	69	92.75%	-->

Files with Coverage Reduction	New Missed Lines	%
sequence_processing_pipeline/GenPrepFileJob.py	5	80.0%
<!--	Total:	5		-->

Totals
Change from base Build 5262144613:	0.3%
Covered Lines:	1671
Relevant Lines:	1884

💛 - Coveralls

charles-cowart commented 1 year ago

@antgonza Just a reminder this should ideally be reviewed after the changes to metapool are approved and merged and the url in setup.py is reverted to normal.

charles-cowart commented 1 year ago

@antgonza ready for re-review!

biocore / mg-scripts