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Restructure output folders to mainly ANNOTATE, SUMMARIZE, and VISUALIZE
Moving and aliad distill to summarize. Move call under annotate and automatically run call when annotate and input_fasta set. If summarize is set, run all distillate sheets, you can still manually set individual distillate sheets the old way. Add QC flag to run QC steps like collect_rna steps, taxa, and others instead of having collect_rna run automatically. BREAKING CHANGE: API changes to move towards using summarize instead of distill, visualize instead of product, traits indead of adjectives, and automatically use call when annotate with input_fasta. QC only ran when directed instead of automatically now as its own flag now.
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[package(pipeline)!: Rename distill to summarize
Moving and aliad distill to summarize.
Move call under annotate and automatically run call when annotate
and input_fasta set.
If summarize is set, run all distillate sheets, you can still
manually set individual distillate sheets the old way.
Add QC flag to run QC steps like collect_rna steps, taxa, and others
instead of having collect_rna run automatically.
BREAKING CHANGE: API changes to move towards using summarize instead
of distill, visualize instead of product, traits indead of adjectives,
and automatically use call when annotate with input_fasta. QC only ran
when directed instead of automatically now as its own flag now.