auto_process_ngs.qc.cellranger

class auto_process_ngs.qc.cellranger.CellrangerCount(cellranger_count_dir, cellranger_exe=None, version=None, reference_data=None)

Wrapper class for handling outputs from cellranger count

The CellrangerCount object gives access to various details of the outputs (such as sample name and file paths).

property cellranger_exe

Cellranger executable

property cmdline

Return the command line used to run ‘cellranger* count’

property cmdline_file

Path to the ‘cellranger* count’ ‘_cmdline’ file

property dir

Path to the directory with the cellranger count outputs

property metrics

Return the appropriate ‘MetricsSummary’ object

property metrics_csv

Path to the cellranger count ‘metrics.csv’ file

property pipeline_name

Pipeline name i.e. name of the software package

property reference_data

Reference dataset

property sample_name

Sample name derived from the directory name

property version

Cellranger version

property web_summary

Path to the cellranger count ‘web_summary.html’ file

class auto_process_ngs.qc.cellranger.CellrangerMulti(cellranger_multi_dir, cellranger_exe=None, version=None, reference_data=None, config_csv=None)

Wrapper class for handling outputs from cellranger multi

The CellrangerMulti object gives access to various details of the outputs (such as sample name and file paths).

property cellranger_exe

Cellranger executable

property cmdline

Return the command line used to run ‘cellranger* count’

property cmdline_file

Path to the ‘cellranger multi’ ‘_cmdline’ file

property config

Return CellrangerMultiConfigCsv instance

property dir

Path to the directory with the ‘cellranger multi’ outputs

metrics(name)

Return a ‘MultiplexSummary’ object for a sample

metrics_csv(name)

Path to the cellranger multi ‘metrics.csv’ file for a sample

property pipeline_name

Pipeline name i.e. name of the software package

property probe_set

Probe set

property reference_data

Reference dataset

property sample_names

Sample names derived from the subdirectory names

property version

Cellranger version

web_summary(name)

Path to the cellranger multi ‘web_summary.html’ file for a sample