Open
Conversation
with limit
Member
|
I think things look ok. Is this the branch we are running on the server? |
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
3 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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Snakefile has been split into 2 branches depending on whether the number of sequences per taxon ("results/fasta/taxon/{taxon}/unaligned.fa") is less than 3, or if it’s equal to or higher than 3. If it’s less than 3, then some rules need to be skipped and such files should be directly passed to the choose_exemplars rule.
choose_exemplars:
The exemplar choosing script is run only if the alignment and tree files exist (so only if the above condition has passed). Otherwise, the outgroups are removed from the input aligned file, which is then used as the output of the rule.
run_raxml:
Updated and adjusted rule, code moved to a python script (run_raxml.py).