Split Snakefile into 2 branches #119
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with limit
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I think things look ok. Is this the branch we are running on the server? |
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Snakefile has been split into 2 branches depending on whether the number of sequences per taxon ("results/fasta/taxon/{taxon}/unaligned.fa") is less than 3, or if it’s equal to or higher than 3. If it’s less than 3, then some rules need to be skipped and such files should be directly passed to the choose_exemplars rule.
choose_exemplars:
The exemplar choosing script is run only if the alignment and tree files exist (so only if the above condition has passed). Otherwise, the outgroups are removed from the input aligned file, which is then used as the output of the rule.
run_raxml:
Updated and adjusted rule, code moved to a python script (run_raxml.py).