Extract jinja_partials and fix CRISPRessoPooled fastp errors
#425
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* Updating README to fix argument, email, and formatting * removing superfluous files * Add link to CRISPRessoPro, move CRISPRessoPro section to end, and fix JSON formatting * Remove link to CRISPRessoPro * Replace Docker badge with link to tags * Add bullet points to Guardrails section and improve formatting * Fix typo and removed colons from guardrails --------- Co-authored-by: Cole Lyman <cole@colelyman.com>
* Extract jinja_partials code * Remove Plotly dependency from setup.py
* Fix replacing flash intermediate files with fastp intermediate files This also moves where the files are added to `files_to_remove` up to near where they are created. * Update to run test branch with paired end Pooled test * Add pooled-paired-sim test to integration tests * Replace flash and trimmomatic with fastp and remove plotly from Github Actions environment * Change test branch back to master
kclem
approved these changes
Apr 24, 2024
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This extracts the functionality needed from
jinja_partialsso that it is no longer a dependency. This also fixes the errors when merging paired end reads using CRISPRessoPooled.