Tool calls \"cellranger aggr\" command to combine output files from \"cellranger count\" (the molecule_info.h5 file from each run) into a single feature-barcode matrix containing all the data. When combining multiple GEM wells, the barcode sequences for each channel are distinguished by a GEM well suffix appended to the barcode sequence. Each GEM well is a physically distinct set of GEM partitions, but draws barcode sequences randomly from the pool of valid barcodes, known as the barcode whitelist. To keep the barcodes unique when aggregating multiple libraries, we append a small integer identifying the GEM well to the barcode nucleotide sequence, and use that nucleotide sequence plus ID as the unique identifier in the feature-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are distinct cell barcodes from different GEM wells, despite having the same barcode nucleotide sequence. This number, which tells us which GEM well this barcode sequence came from, is called the GEM well suffix. The numbering of the GEM wells will reflect the order that the GEM wells were provided in the \"molecule_info_h5\" and \"gem_well_labels\" inputs.

When combining data from multiple GEM wells, the \"cellranger aggr\" pipeline automatically equalizes the average read depth per cell between groups before merging. This approach avoids artifacts that may be introduced due to differences in sequencing depth. It is possible to turn off normalization or change the way normalization is done through the \"normalization_mode\" input. The \"none\" value may be appropriate if you want to maximize sensitivity and plan to deal with depth normalization in a downstream step.

Parameters set by default: --disable-ui - no need in any UI when running in Docker container --id - hardcoded to `aggregated` as we want to return the content of the outputs folder as separate outputs

Skipped parameters: --nosecondary --dry --noexit --nopreflight --description --jobmode --mempercore --maxjobs --jobinterval --overrides --uiport

Not supported features: - Batch correction caused by different versions of the Single Cell Gene Expression chemistry is not supported as the generated metadata file doesn't include \"batch\" field.

Converts Cellranger outputs into the data structure supported by UCSC CellBrowser

Compresses input directory to tar.gz

Compresses input directory to tar.gz

Compresses input directory to tar.gz

Compresses input directory to tar.gz