Let's make cellbender great again!
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… input and output channels with one (because the order of separate channels is not guaranteed)
…handling, and rename processes for clarity; changed work directory name to be nf-work
…directory (users might think that those are cellbender-generated reports)
…ng, and implement helper functions for cell and UMI calculations; introduce count_cells.awk and sort_cells.awk for data processing
…ed parameters, add minimal UMI threshold, and improve script execution with detailed argument passing for RemoveBackground process.
…andling for RemoveBackground process
… in nextflow.config
…r handling and enhance error messaging; update command execution and output directory creation.
…ndling, improve container management, and adjust resource allocation for better performance
…er v0.2 and v0.3: streamline container management and ensure compatibility with updated dependencies.
…ll Ranger and StarSolo outputs with updated sample tables
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Here is a new version of
cellbenderrepository. The following updates were introduced:cellbenderof version0.3.2as well as0.2.2min_umiandexclude_featuresnextflow.configsettings fornextflowprocessescellbenderprocess uses--nvoption for singularity container nowparamsin the processes as it is deprecated nowREADME.mdfile