Based on the PR #323, this PR add the following changes:
Newest GTDB version added for gtdb-tk to make it consistent with the gtdb version used in mmseqs taxonomy
MMseqs taxonomy config added to the production config (fullPipeline_illumina_nanpore_without_aggregate.yml)
EMGB demands the following settings for mmseqs taxonomy: --lca-ranks superkingdom,phylum,class,order,family,genus,species,subspecies . This setting is now part of the default files.
ramMode is now using a boolean instead of a string (false vs. false)
PR review guidelines
Thank you for submitting this PR.
Before merge:
The PR must be reviewed by one of the team members.
Please check if anything in the Readme must be adjusted, or added (development-setup, production-setup, user-guide).
PRs with new modules or workflow interfaces must include tests according to the developer guidelines.
The new code is readable, well commented and should adhere to our developer guidelines.
Before merging it must be checked if a squash of commits is required.
Based on the PR #323, this PR add the following changes:
--lca-ranks superkingdom,phylum,class,order,family,genus,species,subspecies. This setting is now part of the default files.ramModeis now using a boolean instead of a string (falsevs. false)PR review guidelines
Thank you for submitting this PR.
Before merge:
The PR must be reviewed by one of the team members.
Please check if anything in the Readme must be adjusted, or added (development-setup, production-setup, user-guide).
PRs with new modules or workflow interfaces must include tests according to the developer guidelines.
The new code is readable, well commented and should adhere to our developer guidelines.
Before merging it must be checked if a squash of commits is required.