showyourwork / showyourwork

A workflow for reproducible and open scientific articles

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Build up to a rule without necessarily build the article

HealthyPear opened this issue · comments

This is probably related to #316 and/or #298.

I have defined some rules in my Snakefile to e.g. setup additional environment variables to use additional software out of the conda environment, download data files, clean data and go over the next analysis steps.

After reviewing the documentation, it is not clear to me if I can do something like e.g. showyourwork build --rule this_rule and to only (up to) that point of my workflow without worrying about the article (for now).

This should be possible by using directly snakemake, so if you think that it does not make sense to support directly this feature I guess this issue could be closed (but I would add this as a small tip in the documentation).