Phylogenetics tools!

[lkhilton]

Pull Request Checklists

Checklist for New Module

Required

• I used the cookiecutter template and updated the placeholder rules.

• The snakemake rules follow the design guidelines.

  • All references to the rules object (e.g. for input files) are wrapped with str().

• Every rule in the module is either listed under localrules or has the threads and resources directives.

• Input and output files are being symlinked into the CFG["inputs"] and CFG["outputs"] subdirectories, respectively.

• I grouped the input symlinking rule to the next job that uses the input files.

• I updated the final target rule (*_all) to include every output rule.

• I explained important module design decisions in CHANGELOG.md.

• I tested the module on real data for all supported seq_type values.

• I updated the default.yaml configuration file to provide default values for each rule in the module snakefile.

• I did not set any global wildcard constraints. Any/all wildcard constraints are set on a per-rule basis.

• I ensured that all symbolic links are relative and self-contained (i.e. do not point outside of the repository).

• I replaced every value that should (or might need to) be updated in the default configuration file with __UPDATE__.

• I recursively searched for all comments containing TODO to ensure none were left. For example:

  grep -r TODO modules/<module_name>/1.0

If applicable

• I added more granular output subdirectories.

• I added rules to the reference_files workflow to generate any new reference files.

• I added subdirectories with large intermediate files to the list of scratch_subdirectories in the default.yaml configuration file.

• I updated the list of available wildcards for the input files in the default.yaml configuration file.

[Kdreval]

Thanks! Important update!

[Kdreval]

@lkhilton this is merge-able?