Docs Cdiff#128
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Added documentation for the Clostridioides difficile analysis pipeline, detailing requirements, tools, and workflow.
Updated the documentation to clarify the analysis pipeline for Clostridioides difficile, including changes to terminology and additional details on database downloads and analysis steps.
Added SNP identification section detailing the snp_identifier rule and its functionality.
Expanded documentation on deletion identification process, including metadata requirements and evidence evaluation criteria.
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Remnants of Rasmusses final documentation to C. difficile