Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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Feature/stamp stats #59

Closed seb-mueller closed 5 years ago

seb-mueller commented 5 years ago

Experimental debug mode for R-scripts in snakemake

using DEBUG: True flag in config.yaml to produce R-objects in debug folder which can be used for debugging.

Producing barcode summaries to easily compare experiments/samples:

    'summary/barcode_stats_pre_filter.csv',
    'summary/barcode_stats_post_filter.csv',

Example files are attached, (csv was replaced by txt since github doesn't allow csv).

At the moment, I've included the rule into map.smk again, but we should probably create a new rule-file e.g. post-processing.smk or so?

barcode_stats_pre_filter.txt barcode_stats_post_filter.txt