Pipeline: support for large bowtie indexes#238

Merged

taimontgomery merged 10 commits intomasterfrom

Oct 19, 2022

Commits on Oct 14, 2022

Simplifying the user's procedure for activating bowtie-build. Run Config's run_bowtie_build is now an automatically configured value that is triggered by an empty ebwt prefix in the Paths Sheet.
AlexTate
committed
Updating the CWL to collect long bowtie indexes (*.ebwtl) if bowtie-build produces them
AlexTate
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Configuration.setup_ebwt_idx() has been updated for the new bowtie-build activation procedure. If the user defines ebwt but index files can't be found, and they also provided their reference genome…
AlexTate
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Adding execute_post_run_tasks() to Configuration. This function calls others that verify bowtie-build outputs were produced, updates index paths if long indexes were produced, then saves updates to…
AlexTate
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Misc bugfixes addressing changes made in this issue
AlexTate
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Misc small improvements to clarity of code and comments, plus a stability fix for cases where ["reference_genome_files"] contains empty list items
AlexTate
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Adding unit tests for new bowtie index handling procedure
AlexTate
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Documentation updates removing previous bowtie index requirements, and descriptions of the new activation procedure for the bowtie-build step.
AlexTate
committed

Commits on Oct 17, 2022