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Cytoprofiling Optional Arguments

The following arguments are optional additions to a Bases2Fastq execution command for cytoprofiling. Arguments that affect run parameters default to the value that is recorded in the RunParameters.json file from the run.

--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.

bases2fastq /input /output --batch <BATCH_LIST>
bases2fastq /input /output -b <BATCH_LIST>

--cyto-fastq-mask​

Use --cyto-fastq-mask to set a cycle mask for a particular batch in basemask format. The cycles that are included in the cycle mask are also included in the output FASTQ files.

bases2fastq /input /output --cyto-fastq-mask <CYCLE_MASK>

The following example sets cycle mask Y20N* for batch 1 in basemask format:

bases2fastq /input /output --cyto-fastq-mask B01:Y20N*

--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.

bases2fastq /input /output --error-on-missing
bases2fastq /input /output -m

--exclude-tile​

Use --exclude-tile or -e to specify a subset of tiles to exclude from processing. The argument uses regex to identify the tiles. To specify multiple subsets, enter the argument multiple times.

bases2fastq /input /output --exclude-tile '<EXCLUSION_TILES_REGEX>'
bases2fastq /input /output -e '<EXCLUSION_TILES_REGEX>'

The following examples exclude the tiles from lane 1:

bases2fastq /input /output --exclude-tile 'L1R..C..S.'
bases2fastq /input /output -e 'L1R..C..S.'

--flowcell-id​

Use --flowcell-id to overwrite the flow cell ID in the RunParameters.json file with another flow cell ID. Also, you can use this argument to add a missing flow cell ID. Replace FLOWCELL_ID with your flow cell ID.

bases2fastq /input /output --flowcell-id <FLOWCELL_ID>

The following example updates the flow cell ID to 123abc123:

bases2fastq /input /output --flowcell-id <123abc123>

--help​

Use --help or -h to display the usage statement for Bases2Fastq.

bases2fastq --help
bases2fastq -h

--include-tile​

Use --include-tile or -i to specify a subset of tiles to include in the execution. To include specific tiles, you must exclude all tiles with the --exclude-tile or -e argument. The argument uses regex to identify the selected tiles. To specify multiple subsets, enter the argument multiple times.

bases2fastq /input /output --exclude-tile '<EXCLUSION_TILES_REGEX>' --include-tile '<INCLUSION_TILES_REGEX>'
bases2fastq /input /output -e '<EXCLUSION_TILES_REGEX>' -i '<INCLUSION_TILES_REGEX>' -i '<INCLUSION_TILES_REGEX>'

The following example includes the subset of tiles L1R..C..S2 after excluding all tiles:

bases2fastq /input /output --exclude-tile 'L.*R..C..S.' --include-tile 'L1R..C..S2'

The following example includes the additional subset of tiles L2R..C..S1:

bases2fastq /input /output -e 'L.*R..C..S.' -i 'L1R..C..S2' -i 'L2R..C..S1'

--input-remote​

Use --input-remote to set the rclone remote name for the remote INPUT_DIRECTORY.

bases2fastq /input /output --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
bases2fastq /input /output --log-level <MIN_LOG_LEVEL>
bases2fastq /input /output -l <MIN_LOG_LEVEL>

--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.

bases2fastq /input /output --no-error-on-invalid
bases2fastq /input /output -n

--num-threads​

Use --num-threads or -p 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.

bases2fastq /input /output --num-threads <NUMBER_OF_THREADS>
bases2fastq /input /output -p <NUMBER_OF_THREADS>

The following example specifies 10 threads to use for processing:

bases2fastq /input /output --num-threads 10
bases2fastq /input /output -p 10

--output-remote​

Use --output-remote to set the rclone remote name that points to the output files.

bases2fastq /input /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.

bases2fastq /input /output --panel <PATH/TO/ALTERNATE_PANEL.JSON>
bases2fastq /input /output -p <PATH/TO/ALTERNATE_PANEL.JSON>

--per-target-fastq​

Use --per-target-fastq to generate FASTQ files for each cell assignment target in each cytoprofiling batch.

bases2fastq /input /output --per-target-fastq

--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.

bases2fastq /input /output --run-manifest <PATH/TO/CORRECTED_MANIFEST.CSV>
bases2fastq /input /output -r <PATH/TO/CORRECTED_MANIFEST.CSV>

--tca-manifest​

Use --tca-manifest to define an alternate target cell assignment manifest file. The file must be in .csv format.

bases2fastq /input /output --tca-manifest <PATH/TO/ALTERNATE_TCA_MANIFEST.CSV>

--version​

Use --version or -v to display the current Bases2Fastq version. Bases2Fastq logs the version at the start of any execution on the command line and in the log file.

bases2fastq --version
bases2fastq -v

--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.
bases2fastq /input /output --well <WELL_LOCATIONS>
bases2fastq /input /output -w <WELL_LOCATIONS>

The following examples specify wells A1,B2,C3,D4:

bases2fastq /input /output --well A1,B2,C3,D4
bases2fastq /input /output -w A1,B2,C3,D4
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