25-274

Here is a brief list of updates:

• The pipeline now uses .csv file instead of .tsv as an input. I noticed that it was challenging for users outside of cellgeni to generate those
• Removed --mapper and --solo_quant parameters as pipeline now handles any type of input: CellRanger/STARsolo output directory (works for all flavors of CellRanger), .h5 file, .mtx directory. For more details see examples/sample_table.csv file.
• Added --mapper_preset option to choose parameters for CellBender from CellRanger/STARsolo filtering (needs full output directory)
• You can provide several modalities to --exclude_features "Peaks,Multiplexing Capture,CRISPR Guide Capture" parameter now
• Added --ignore_extensions parameter to ignore some any file types when loading data from iRODS. Targeted at heavy .bam files
• I also converted cellbender and irods processes to nf-core and added some tests for them. You can find all test data on iRODS: /archive/cellgeni/tests

For more details read README.md file