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Optional Arguments

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

Select a hyperlinked argument to see an example execution command.

--chemistry-versionOverwrite the sequencing kit version. Valid values are 1 for a version 1 kit or Cloudbreak for a Cloudbreak™ kit.RunParameters.json
--demux-only, -dEnable demultiplexing-only mode, which performs demultiplexing and outputs index metrics without generating any FASTQ files.False
--detect-adaptersDetect adapters sequences. If you are using this argument, Bases2Fastq overrides any sequences present in the run manifest.False
--exclude-tile, -eUse regular expression (regex) to specify a subset of tiles to exclude from processing (e.g., L1.*C02S.). To specify multiple subsets, enter the argument multiple times.Not applicable
--filter-maskApply a custom base mask to specify the cycles that determine if a read passes filter (PF). The argument is only compatible with Cloudbreak chemistry. For information on base masks, see the Run Manifest Documentation.Not applicable
--flowcell-idOverwrite the flow cell ID used for a run.RunParameters.json
--force-index-orientationPerform demultiplexing without detecting the index sequence orientation. When true, Bases2Fastq applies the orientation recorded in the run manifest.False
--help, -hDisplay the usage statement.Not applicable
--i1-cyclesOverwrite the number of cycles in Index 1.RunParameters.json
--i2-cyclesOverwrite the number of cycles in Index 2.RunParameters.json
--include-tile, -iUse regex to specify a subset of tiles for processing after excluding all tiles from processing (e.g., --exclude-tile ".*" --include-tile "L1.*C02S."). To specify multiple subsets, enter the argument multiple times.Not applicable
--input-remoteSet the rclone remote name that points to the input files.Not applicable
--kit-configurationOverwrite the kit configuration. Valid values are 150Cycles for a 2 x 75 kit or 300Cycles for a 2 x 150 kit.RunParameters.json
--legacy-fastqApply a legacy file naming convention to FASTQ files, such as SampleName_S1_L001_R1_001.fastq.gz.False
--log-level, -lSpecify the minimum level required to log an event: INFO, DEBUG, WARNING, or ERROR.INFO
--no-projectsOrganizes the output file directory without project folders and instead uses the standard, sample-based folder structure.Not applicable
--num-threads, -pSpecify the number of threads to use for processing. The minimum value is 1 and the maximum value depends on your system.1
--num-unassignedSpecify a value ≤ 1000 that indicates the maximum number of unassigned sequences to support.30
--output-remoteSet the rclone remote name that points to the location of the FASTQ files and other outputs.Not applicable
--preparation-workflowOverwrite the library prep workflow. Valid values are Adept and Elevate.RunParameters.json
--qc-onlyEnable QC-only mode, which generates a representative view of run metrics on one tile and no FASTQ files.False
--r1-cyclesOverwrite the number of cycles in Read 1.RunParameters.json
--r2-cyclesOverwrite the number of cycles in Read 2.RunParameters.json
--run-manifest, -rDefine the location of an alternate run manifest for the execution instead of the RunManifest.csv file output by the instrument.Not applicable
--settingsOverwrite run manifest settings by entering the argument for each setting you want to overwrite. Available settings are in the Run Manifest Documentation. For example:
  • --settings "I1Fastq,True"
  • --settings "I2Fastq,True"
  • --settings "I1Mask,I1:N3Y*"
Not applicable
--skip-qc-reportDo not create an HTML QC report.False
--split-lanesDivide FASTQ files by flow cell lane.False
--strict, -sEnable strict mode, which prevents processing when any input files are invalid. When strict mode is off, Bases2Fastq warns you that files are missing or corrupt but continues processing.False
--version, -vDisplay the current version of Bases2Fastq. Bases2Fastq logs the version at the start of FASTQ file generation regardless of whether you include this argument.Not applicable