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Feature/228 support for celda decontx #230
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… params.sc.file_converter.off Update add off param and set it to seurat_rds in tenx_atac_cellranger_mex.config
…r the file converter to use
Improve code in SC__FILE_CONVERTER process
…iltering This regards the SC__PREPARE_OBS_FILTER and SC__APPLY_OBS_FILTER processes
…e.g.: h5ad): SC__FILE_CONVERTER_FROM_SCE Plus remove unused process SC__FILE_CONVERTER_HELP
…. This allows to have multiple SC__FILE_CONVERTER with different output formats running within 1 pipeline.
…lParams instead of the toolKey
…config: run single_sample_scrublet along with decontx [celda] pipelines. The scrublet workflow is applied on the DecontX filtered data.
…rting 10x_cellranger_mex to sce_rds. And add logic for tagging the cell with sample id for that conversion.
…pipeline both with Scrublet and DecontX data
pcacv: Minor changes scrublet: Check for NA values and fill them so that num doublets can be calculated at end of notebook
…with "SC" default argument
… each sample: SC__CELDA__DECONTX_MERGE_OUTLIER_TABLES
…_scrublet and add new profile single_sample_decontx_correct_scrublet to run.
…"bad" (i.e.: cells likely containing ambient RNA)
…crublet pipelines
…e_decontx_scrublet
…gle_sample_decontx_scrublet
…single_sample_decontx_scrublet
dweemx
added
documentation
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Closes #228