v1.3.0 #24
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v1.3.0 #24
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Ensures usage of a specific solver (Clarabel) by default and sets environment variables for all its internal linear system solvers
Fix plot design source Update sample sorting Update demix table column names Fix column names Update temp variable name Update structure
Simplify TSV concatenation and reuse a rule. This avoids problems and allows reusing the rule for any other set of tables.
Harmonize use of output/report and workflow/scripts/report directories for report-specific stuff.
Also adds demix option to restrict the maximum depth passed to samtools mpileup
Also updates the order in the configuration file
This accounts for the two processes spawned by samtools and ivar, which can lead to higher than expected CPU usage
Renames outgroup params for distance tree rules
Also fixes CSS as input
Fixes legend in context phylogeny and updates colors in diversity plot
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