Fix: Make it so that bamlist generation is re-run if sample order changes, keeping meta-data consistent #51
Conversation
This file contains 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
This will force a rerun of the rule. I am not quite sure why it wouldn't before. The code should change if input order changes, but maybe Snakemake doesn't look inside input list expansions when determining code changes?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
If sample order changed in the samples.tsv after a completed run, and a new run was made, poplists would be re-generated, but not bamlists, which would cause samples info to line up with the wrong samples in the beagle files. Now, the bamlist will also be generated. This is not the most efficient way to handle this, as it will trigger many re-runs, but it seems a safe way without changing how GL files are made in the workflow. This should only trigger when samples are being changed anyway, so re-runs are mostly going to be desired anyway.
Closes #48.