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DSL2: Print Nuclear Contamination JSON N/A value #995

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TCLamnidis opened this issue Jun 7, 2023 · 2 comments
Open

DSL2: Print Nuclear Contamination JSON N/A value #995

TCLamnidis opened this issue Jun 7, 2023 · 2 comments
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bug Something isn't working DSL2
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@TCLamnidis
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The print nuclear contaminatino script produces a JSON with the results, in which the na value is set to "N/A". This should be replaced with a valid JSON missing value (null?) so that loading of the JSON for downstream processing does not raise errors (strings vs floats).

@TCLamnidis TCLamnidis added bug Something isn't working DSL2 labels Jun 7, 2023
@TCLamnidis TCLamnidis changed the title Print Nuclear Contamination JSON N/A value DSL2: Print Nuclear Contamination JSON N/A value Jun 7, 2023
@TCLamnidis
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See multimeric/TidyMultiqc#9 for a similar issue with NaNs

@scarlhoff
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scarlhoff commented Jun 23, 2023

As of #1004, we now print "none" in the nuclear_contamination.txt and "null" in the nuclear_contamination.json. Will need to observe how MultiQC behaves

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