Optional arguments
The following arguments are optional additions to a Cells2Stats execution command:
--batch
Use --batch or -b to restrict analysis to batch(es) that match the comma-delimited list of batches. Allowed values are B1-B8, based on how many batches are present in the run.
cells2stats /input --batch <BATCH_LIST>
cells2stats /input -b <BATCH_LIST>
--bases2fastq
Use --bases2fastq or -B to specify the path to the Bases2Fastq™ binary to use. This is an external dependency that is used to generate FASTQ files during OPS analysis.
cells2stats /input --bases2fastq <PATH_TO_BASES2FASTQ_BINARY>
cells2stats /input -B <PATH_TO_BASES2FASTQ_BINARY>
--bowtie
Use --bowtie to specify the path to the Bowtie binary to use. This is an external dependency that is used in Optical Pooled Screen analysis.
cells2stats /input --bowtie <PATH_TO_BOWTIE_BINARY>
--bowtie-build
Use --bowtie-build to specify the path to the Bowtie-build binary to use. This is an external dependency that is used in Optical Pooled Screen analysis.
cells2stats /input --bowtie-build <PATH_TO_BOWTIE_BUILD_BINARY>
--build-viz-from-SDO
Use --build-viz-from-SDO to generate visualization files from a Spatial Data Object (SDO). This flag takes an SDO as input and produces merged parquet files and a visualization index. Use this option to regenerate visualization files for an existing SDO where visualization generation previously failed.
cells2stats /input --build-viz-from-SDO <PATH/TO/SDO>
--cellprofiler
Use --cellprofiler or -c to specify the path to the CellProfiler utility to use. This is an external dependency that is used to generate morphology metrics. If you do not want to specify a CellProfiler utility and do not have CellProfiler installed, then run with --skip-cellprofiler.
cells2stats /input --cellprofiler <PATH/TO/CELLPROFILER>
cells2stats /input -c <PATH/TO/CELLPROFILER>
--error-on-missing
Use --error-on-missing or -m to terminate an execution for a missing file. By default, missing files are skipped and execution continues.
cells2stats /input --error-on-missing
cells2stats /input -m
--help
Use --help or -h to display the usage statement for Cells2Stats.
cells2stats --help
cells2stats -h
--input-remote
Use --input-remote to set the rclone remote name for the remote INPUT_DIRECTORY.
cells2stats /input --input-remote '<INPUT_DIRECTORY_NAME>'
--log-level
Use --log-level or -l to specify the minimum level required to log an event. The default value is INFO. Use one of the following valid values:
INFODEBUGWARNINGERROR
cells2stats /input --log-level <MIN_LOG_LEVEL>
cells2stats /input -l <MIN_LOG_LEVEL>
--max-unassigned
Use --max-unassigned or -u to limit the number of unassigned sequences that are reported, from 1-10000 sequences. By default, the value is set to 30.
cells2stats /input --max-unassigned <MAX_UNASSIGNED_SEQUENCES>
cells2stats /input -u <MAX_UNASSIGNED_SEQUENCES>
--no-error-on-invalid
Use --no-error-on-invalid or -n to skip invalid files and continue execution. By default, missing files are skipped and execution continues.
cells2stats /input --no-error-on-invalid
cells2stats /input -n
--num-threads
Use --num-threads or -j to specify the number of threads to use for processing, with a minimum value of 1 and a maximum value that is based on your system. The default value is 1.
cells2stats /input --num-threads <NUMBER_OF_THREADS>
cells2stats /input -j <NUMBER_OF_THREADS>
The following examples specify 8 as the number of threads to use for processing:
cells2stats /input --num-threads 8
cells2stats /input -j 8
--output
Use --output or -o to specify the location to save the output to. The default location is the INPUT_RUN_DIRECTORY/CYTOPROFILING/<TIMESTAMP> folder.
cells2stats /input --output <PATH/TO/OUTPUT_LOCATION>
cells2stats /input -o <PATH/TO/OUTPUT_LOCATION>
--output-remote
Use --output-remote to set the rclone remote name that points to the output files.
cells2stats /input -o /output --output-remote '<OUTPUT_DIRECTORY_NAME>'
--panel
Use --panel or -p to define an alternate panel.json file location, instead of the panel.json file output by the instrument. The file path can direct to a local or remote location.
cells2stats /input -o /output --panel <PATH/TO/ALTERNATE_PANEL.JSON>
cells2stats /input -o /output -p <PATH/TO/ALTERNATE_PANEL.JSON>
--python
Use --python or -P to set the path of the python version to execute.
cells2stats /input -o /output --python <PATH/TO/PYTHON_VERSION>
cells2stats /input -o /output -P <PATH/TO/PYTHON_VERSION>
--run-manifest
Use --run-manifest or -r to define the location of an alternate run manifest for the execution instead of the RunManifest.csv file output by the instrument. For more information on corrected run manifests, see the Run Manifest Documentation.
cells2stats /input -o /output --run-manifest <PATH/TO/CORRECTED_MANIFEST.CSV>
cells2stats /input -o /output -r <PATH/TO/CORRECTED_MANIFEST.CSV>
--samtools
Use --samtools to specify the path to the Samtools binary to use. This is an external dependency that is used in Optical Pooled Screen analysis. For more information, see the Samtools documentation.
cells2stats /input --samtools <PATH/TO/SAMTOOLS_BINARY>
--segmentation
Use --segmentation or -S to pass in a directory of alternative cell segmentation masks. For more information on how to create a directory of cell segmentation masks, see the Resegmentation Using Python tutorial and see the expected format of an Alternative Cell Segmentation Directory.
cells2stats /input -o /output --segmentation <PATH/TO/ALTERNATIVE_CELL_SEGMENTATION_DIRECTORY>
cells2stats /input -o /output -S <PATH/TO/ALTERNATIVE_CELL_SEGMENTATION_DIRECTORY>
--skip-cellprofiler
Use --skip-cellprofiler to skip the execution of CellProfiler. This saves execution time and allows you to run Cells2Stats without a CellProfiler dependency. When you skip the execution of CellProfiler, morphology features will not be generated in your RawCellStats.csv or RawCellStats.parquet files.
cells2stats /input --skip-cellprofiler
cells2stats /input -s
--skip-html-report
Use --skip-html-report or -H to skip the creation of the MultiQC HTML report.
cells2stats /input --skip-html-report
cells2stats /input -H
--specialized-targeted-min-query-length
Use --specialized-targeted-min-query-length to set the minimum query-length gate, in bases, for specialized targeted alignments. The gate applies to all target sites. By default, the gate per site is the number of bases represented by the target mask, which is the spacer sequence length. The minimum allowed value is 12. If the value exceeds the mask sequence length of a given target, Cells2Stats logs a warning.
cells2stats /input --specialized-targeted-min-query-length <LENGTH>
--tca-manifest
Use --tca-manifest to define an alternate target cell assignment manifest file. The file must be in .csv format.
cells2stats /input --tca-manifest <PATH/TO/ALTERNATE_TCA_MANIFEST.CSV>
--target-mismatch-threshold
Use --target-mismatch-threshold to override the Bowtie mismatch tolerance applied to all target sites during Optical Pooled Screen (OPS) analysis. By default, the mismatch tolerance for each target site is read from the target cell assignment manifest. When set, this flag overrides any per-target TargetMismatchThreshold values in the manifest and applies to every target site. Allowed values are 0, 1, 2, or 3.
cells2stats /input --target-mismatch-threshold <N>
--tile
Use --tile or -t to specify the tiles to run on. The argument uses regex to identify the selected tiles. To specify multiple subsets, enter the argument multiple times.
cells2stats --tile <TILES_REGEX>
cells2stats -t <TILES_REGEX>
The following example includes the subset of tiles in Lane 1 L1R..C..S.:
cells2stats --tile 'L1R..C..S.'
--verbose-transfer
Use --verbose-transfer, -T to print file names to the terminal when logs are copied.
cells2stats --verbose-transfer, -T
--version
Use --version or -v to display the current Cells2Stats version. Cells2Stats logs the version at the start of any execution on the command line and in the log file.
cells2stats --version
cells2stats -v
--viz-points-sort-memory-gb
This is an advanced option. Most users do not need to set this option.
Use --viz-points-sort-memory-gb to set the memory, in gigabytes (GB), allocated for points sorting during Spatial Data Object (SDO) generation. If SDO generation fails with an out-of-memory error, adjust this value based on the available memory on your system. By default, this value is set to 16. Element recommends setting this to half of your available system memory.
cells2stats /input --viz-points-sort-memory-gb <GB_MEMORY>
--viz-points-sort-threads
This is an advanced option. Most users do not need to set this option.
Use --viz-points-sort-threads to set the number of threads used for points sorting during Spatial Data Object (SDO) generation. By default, this value is set to a fraction of the --num-threads value. To further optimize performance, use this option to adjust CPU usage during points sorting. Continue adjusting until SDO generation completes successfully.
cells2stats /input --viz-points-sort-threads <CPU_THREADS>
--viz-shape-smoothing-workers
This is an advanced option. Most users do not need to set this option.
Use --viz-shape-smoothing-workers to set the number of workers used for shape smoothing during Spatial Data Object (SDO) generation. By default, this value is set to a fraction of the --num-threads value. To further optimize performance, use this option to adjust CPU usage during shape smoothing. Continue adjusting until SDO generation completes successfully.
cells2stats /input --viz-shape-smoothing-workers <CPU_WORKERS>
--well
Use --well or -w to specify which well or wells to use for a run. Use the following valid values:
- For a 12-well consumable, use A1-F2.
- For a 48-well consumable, use A1-L4.
cells2stats --well <WELL_LOCATIONS>
cells2stats -w <WELL_LOCATIONS>
The following example includes wells A1, A2, and B1:
cells2stats --well A1,A2,B1
cells2stats -w A1,A2,B1