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Singleplex Flex data cannot be processed because probeset file is not added to config

#515Opentgelafr-pfzr 创建于 2026-01-12
bug
T
tgelafr-pfzrcommented
### Description of the bug The pipeline isn't processing the probeset unless a cellranger multi barcodes sheet is provided, which shouldn't be necessary for singleplexed data. This is a module-level issue occurring here: https://github.com/nf-core/scrnaseq/blob/f7bf36d7c7e4bddc5302c3facd8d19ca83e22226/modules/nf-core/cellranger/multi/main.nf#L79. Singleplex flex _is_ permitted by cellranger (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-flex-multi-frp#sfrp-onebc), and modifying this single line has allowed my runs to finish succesfully. ### Command used and terminal output ```console ``` ### Relevant files _No response_ ### System information _No response_
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