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