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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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Test workflow with Bioc3.19 images #746

Closed jashapiro closed 2 months ago

jashapiro commented 4 months ago

The next versions of scpcaTools docker images, following the implementation of https://github.com/AlexsLemonade/scpcaTools/pull/269 and possibly https://github.com/AlexsLemonade/scpcaTools/pull/270, are currently planned to use Bioconductor 3.18. This release included a number of changes, which would not necessarily be expected to have large effects, but still could, of course!

Some of the most significant changes may be to zellkonverter, which includes a new version of AnnData (0.10), which does seem to change the output format a bit. With luck, this may also address the issue we had with exporting large objects. Nothing in the release notes seems to directly address this, but the changes may be significant enough to make a difference.

jashapiro commented 2 months ago

This was effectively completed by https://github.com/AlexsLemonade/scpca-nf/pull/763