Add snippy multiple alignment and iqtree #37
Description
In sbx_sga_snippy, add new rules to run snippy-core to create a multiple alignment of all samples and then iqtree for building a phylogeny.
Input should be all of the dirs ISOLATE_FP / "snippy" / "{sample}" and output should be the core.full.aln file.
cd $(dirname {output}) && snippy-core --prefix core {input}
Input should be the core.full.aln file and the output should be the core.full.aln.treefile file (in the same directory).
iqtree -s core.full.aln -m MFP -B 1000 -T AUTO -pre $(dirname {input})