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AlexsLemonade / scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
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[BUG] Age in sample_metadata is inconsistently typed #735

Closed jashapiro closed 6 months ago

jashapiro commented 7 months ago

Describe the bug

In the metadata(sce)$sample_metadata table, we sometimes have the age column as a double and sometimes a character.

To reproduce Using the processed output files for two libraries: 

> type(metadata(SCPCL000822)$sample_metadata$age)
[1] "double"
> type(metadata(SCPCL000608)$sample_metadata$age)
[1] "character"

Expected behavior

Always one type!

Version information

I believe these outputs are from the latest scpca-nf output, but I am not sure... we should check with 0.8.0 outputs

Additional context

The error could easily be in scpcaTools; I have not yet gone to look at where the data is read in.

allyhawkins commented 7 months ago

For some reason I thought we had fixed this, but it gets read in here and we don't specify everything be a character, which we probably should. https://github.com/AlexsLemonade/scpca-nf/blob/8bef82d853d19e5aeddd75401aa54cf8bfbced13/bin/generate_unfiltered_sce.R#L164

jashapiro commented 7 months ago

We probably fixed it somewhere else...

allyhawkins commented 6 months ago

Closed by #738