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parseWBHeader extract Snakemake env config variables #9

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stefanches7 opened this issue Aug 7, 2018 · 1 comment
Open
3 tasks

parseWBHeader extract Snakemake env config variables #9

stefanches7 opened this issue Aug 7, 2018 · 1 comment
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@stefanches7
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  • Call Python code from R
  • Use Snakemake Python API to construct the appropriate object
  • Copy over the attributes (merge)
@stefanches7 stefanches7 changed the title parrseWBHeader extract Snakemake env config variables parseWBHeader extract Snakemake env config variables Aug 16, 2018
@stefanches7
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So, the Snakemake API as such is now restricted to the one and only workflow call, which returns only boolean status of workflow (success/ failure). So no way to parse config values from some sm object itself that I see @kTakumo . It could be that there is some doubtful pythonic magic code to debug the function, but I don't come up with any idea.
What we can is read configfile of Snakefile, if it is there, and construct config out of it.

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