Cell Screening optional arguments

Optional arguments used for multiomic run inputs

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

Note:

The following sequencing arguments are not valid for cell screening runs, and Bases2Fastq terminates the execution if you use them: --chemistry-version, --detect-adapters, --force-detect-index-orientation, --force-index-orientation, --group-fastq, --i1-cycles, --i2-cycles, --kit-configuration, --legacy-fastq, --preparation-workflow, --r1-cycles, --r2-cycles, and --settings.

--batch

Use --batch to restrict analysis to the batches in a comma-delimited list, such as B01,B02,B03. Batch names match the batches present in the run. You cannot combine --batch with --cyto-fastq-mask.

bases2fastq /input /output --batch <BATCH_LIST>

The following example restricts analysis to batches B01 and B02:

bases2fastq /input /output --batch B01,B02

--bgzf-compression

Use --bgzf-compression to write FASTQ files with blocked GNU zip format (BGZF) compression instead of standard single-member gzip compression. For each .fastq.gz file, Bases2Fastq also writes a .fastq.gz.gzi index file that is compatible with bgzip. BGZF files remain readable by any gzip-compatible tool.

bases2fastq /input /output --bgzf-compression

--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. To set masks for multiple batches, enter the argument multiple times. You cannot combine --cyto-fastq-mask with --batch or --per-target-fastq.

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 to terminate an execution for a missing file. By default, missing files are skipped and execution continues.

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

--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.'

--filter-mask

Use --filter-mask to calculate the filter status of polonies for specific batches from the base calls, instead of reading the filter files in BaseCalling/Filter/. Specify a base mask for each batch, and separate each batch mask with a hyphen.

• Bases2Fastq calculates the filter status for each batch in the mask with the same rule as primary analysis, using a quality threshold of 6.
• Batches that are not in the mask use the filter files in BaseCalling/Filter/. If every processed batch is in the mask, the BaseCalling/Filter/ directory is not required.
• The info/Bases2Fastq.log file records the filter source for each batch.
• If the mask includes a batch that --batch excludes, Bases2Fastq logs a warning and does not apply the mask for that batch.

bases2fastq /input /output --filter-mask <FILTER_MASK>

The following example calculates filter status from cycles 6–20 of batch B01 and cycle 1 of batch B02:

bases2fastq /input /output --filter-mask 'B01:N5Y15N*-B02:YN*'

--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

--group-well-label

Use --group-well-label to group FASTQ files by the well label defined in the run manifest, per batch. Bases2Fastq writes the FASTQ files to Samples/{WellLabel} and names each file {WellLabel}_{Batch}_R1.fastq.gz.

bases2fastq /input /output --group-well-label

--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 to skip invalid files and continue execution. By default, Bases2Fastq terminates an execution when a file is invalid.

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

--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 to define an alternate panel file location, instead of the Panel.json file output by the instrument. The path can be local or remote. Bases2Fastq copies the panel file to the output directory as Panel.json.

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

--per-target-fastq

Use --per-target-fastq to generate FASTQ files for each cell assignment target in each cell screening batch, according to the FASTQ masks in the target cell assignment manifest. You cannot combine --per-target-fastq with --cyto-fastq-mask.

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>

--segmentation

Use --segmentation to pass in a directory of alternative cell segmentation masks for use during multiomic FASTQ generation. The directory can be local or remote. Bases2Fastq accepts segmentation masks as TIFF files or as a Zarr v3 store, and logs the detected format to info/Bases2Fastq.log. For more information on how to create a directory of cell segmentation masks, see the Resegmentation Using Python tutorial.

bases2fastq /input /output --segmentation <PATH/TO/CELL_SEGMENTATION_DIRECTORY>

--skip-empty-fq-files

Use --skip-empty-fq-files to skip generation of FASTQ files with zero reads. By default, Bases2Fastq generates an empty FASTQ file for each output with zero reads.

bases2fastq /input /output --skip-empty-fq-files

--skip-qc-report

Use --skip-qc-report to skip the creation of the HTML QC report.

bases2fastq /input /output --skip-qc-report

--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 to specify which well or wells to use for a run as a comma-delimited list. 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>

The following example specifies wells A1, B2, C3, and D4:

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