Updated ichorcna to allow for more flexibility in reference wigs (though ended up being a moot change for grch37-noalt); updated reference workflow to include hg19-reddy_masked.

Note that chrY info is needed for ichorCNA to complete. In the case of grch37-noalt (with no chrY), added extra lines in the wig to denote 0 coverage for chrY.

Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

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.

Checklist for Updated Module

Important! If you are updating the module version, ensure the previous version of the module is restored from master.
If you want to restore a deleted file or directory from the remote master, you can use git checkout origin/master path/to/file,
then a git commit will ensure that file is tracked on your branch again.
Example:

mv modules/strelka/1.1 modules/strelka/1.2
git checkout origin/master modules/strelka/1.1