Pipeline: support for large bowtie indexes#238
Merged
taimontgomery merged 10 commits intomasterfrom Oct 19, 2022
Merged
Conversation
…fig's run_bowtie_build is now an automatically configured value that is triggered by an empty ebwt prefix in the Paths Sheet.
…uild produces them
…ild activation procedure. If the user defines ebwt but index files can't be found, and they also provided their reference genome files, then the pipeline will automatically rebuild the indexes and update the Paths Sheet at the end of the end-to-end run. setup_ebwt_idx() has also been significantly refactored and cleaned up. It has been bugging me for a long time and it feels good to see it in better shape.
… others that verify bowtie-build outputs were produced, updates index paths if long indexes were produced, then saves updates to the Paths Sheet and Run Config. This addresses a long running problem where end-to-end runs with a bowtie-build step would not save the updated ebwt in Paths Sheet if a downstream step produced an error. Now, the updated ebwt path is written to the Paths File at the end of any run where at least bowtie-build ran successfully.
…lity fix for cases where ["reference_genome_files"] contains empty list items
…d descriptions of the new activation procedure for the bowtie-build step.
# Conflicts: # README.md
Collaborator
|
Minimal testing since I didn't have ebwtl index files to work with. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Support for large bowtie indexes (*.ebwtl) has been folded into routines that handle these files.
This PR also has some general improvements for the bowtie-build step:
Note: this branch was started from issue-235 so until its PR is closed this PR will also include changes from that branch
Closes #237