Matrix table fix #7
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Fixes #6
Issue occurs when running gubbins on clusters with less than 3 isolates. There is a parameter to skip_gubbins but we only want to skip if there are 2 isolates in a cluster. In production the pipeline is wrapped in a script and not able to be manually updated each time.
Changes:
Adds a boolean value called 'run_gubbins' in snippy_core.nf , set to true if there are 3 or more isolates in the snippy_dirs
Adds to gubbins.nf to run process only when run_gubbins is true, adds errorStrategy 'ignore'
In main.nf, adds run_gubbins variable to gubbins process, and assigns ch_alignment to the gubbins output only if run_gubbins is true, otherwise the snippy core alignment is used