Extended features

The workflow now includes the following features:

1. Addition of the ICE gene pairs similar to the RPA assay, and removal of the requirement for contig assembly.
2. Adding the new macrolide resistance gene estT (it is in the updated AMR databases).
3. Adding Bibersteinia trehalosi to the list of BRD organisms the internal report.
4. Adding the virulence gene (ibpA) for Histophilus somni in the same way that we check for Mannheimia serotypes.
5. ARG database update (and automation of the update process).

Reproduction 2

Set up automated testing (diffing output report sheets) via the diff_report_sheets rule.

Readability

Formatted code, removed unnecessary comments and obsolete code, and moved documentation into Snakemake rule docstrings.

Portability

This version automatically builds custom databases and installs all dependencies (works on local servers). Also, the sample_summary script/rule now takes a TSV file with relevant file paths instead of looking for them via hard-coded paths within the script.

Reproduction

This version runs to completion on Lael's account on cedar.computecanada.ca. It appears to reproduce both internal and clinician reports as expected. Software dependencies and databases are installed variously via environment modules, python virtual environments (via pip), and installation from source by rules. At this point, it is somewhat unclear whether the mh_ribosomal_muts rule is working correctly (it had to be modified to run to completion) and whether the AMR databases are the same as those used in the workflow on the USask server.