Add sccmec module

[Emkago]

Description

I have added a tool for typing SCCmec cassettes in assemblies of Staphylococcus species.

Summary of the changes made:

• added a new module
• included the module in S. aureus workflow
• edited config files

Primary function of PR

• Hotfix
• Minor functionality improvement
• Major functionality improvement / New type of analysis
• Backward-breaking functionality

Testing

I have tested it with Nanopore test data.

Sign-offs

• Code reviewed by @octocat
• Code tested by @octocat

[Emkago]

Analysis is currently not limited to short- or long-read track, but it can be changed later if desired. Results of the analysis are available in the output folder, but are not (yet) reported in the final json file.

[ryanjameskennedy]

Analysis is currently not limited to short- or long-read track, but it can be changed later if desired. Results of the analysis are available in the output folder, but are not (yet) reported in the final json file.

Yeah you would have to add the parsing of the output file to bonsai-prp. I have already made an issue.

[Emkago]

I see you have changed reporting of the version of the tool. Have you seen that it reports verisons of 3 components? Output looks like this:

sccmec --version
camlhmp, version 1.1.0
schema sccmec_targets, version 1.2.0
schema sccmec_regions, version 1.2.0

[ryanjameskennedy]

I see you have changed reporting of the version of the tool. Have you seen that it reports verisons of 3 components? Output looks like this:

sccmec --version
camlhmp, version 1.1.0
schema sccmec_targets, version 1.2.0
schema sccmec_regions, version 1.2.0

Indeed, all we want is the version number (X.X.X format, excl. software name, etc.) that matches the tool version number (which will either be targets/regions).

[ryanjameskennedy]

LGTM! When you have added a parsing function to bonsai-prp, then you can create another PR to JASEN to include it in output:)