no way to force exit jupyter nb execution via papermill

broadinstitute / epi-SHARE-seq-pipeline

Epigenomics Program pipeline to analyze SHARE-seq data.

MIT License

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no way to force exit jupyter nb execution via papermill #108

Closed sidwekhande closed 1 year ago

sidwekhande commented 1 year ago

Cannot find a way to force exit jupyter notebook running IRkernel via papermill. This mainly affects the DORCs correlation function, which goes into an infinite loop if there are no common barcodes between RNA and ATAC matrices.

papermill ignores R system quit() , stop() commands

sidwekhande commented 1 year ago

adding quit(1) exits execution but not in a clean manner

sidwekhande commented 1 year ago

using a combination of stop() and return NULL inside error()