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>

--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:

• INFO
• DEBUG
• WARNING
• ERROR

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 sequenced 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 thread 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

--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>

--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

--visualization

Use --visualization or -V to create CytoCanvas™ input files as part of the Cells2Stats output. Use this command if you have a directory of alternative segmentation masks that you want to perform target to cell assignment and regenerate all cell statistics files and visualization files. Otherwise, you can use use --visualization-only.

cells2stats /input --visualization -S <PATH/TO/ALTERNATIVE_CELL_SEGMENTATION_DIRECTORY>

cells2stats /input -V -S <PATH/TO/ALTERNATIVE_CELL_SEGMENTATION_DIRECTORY>

--visualization-only

Use --visualization-only or -O to create CytoCanvas input files as the Cells2Stats output without performing target to cell assignment or regenerating cell statistics files. Use this command if you want to prepare your original run output for visualization in CytoCanvas.

cells2stats /input --visualization-only

cells2stats /input -O

--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