```
docker run --rm docker.io/elembio/bases2fastq:2.3 bases2fastq -h
```

Usage: bases2fastq [OPTIONS] ANALYSIS_DIRECTORY OUTPUT_DIRECTORY

positional arguments:
        ANALYSIS_DIRECTORY                Location of analysis directory
        OUTPUT_DIRECTORY                  Location to save output

optional arguments:
        --chemistry-version VERSION       Run parameters override, chemistry version.
        --demux-only, -d                  Generate demux files and indexing stats without generating FASTQ
        --detect-adapters                 Detect adapters sequences, overriding any sequences present in run manifest.
        --error-on-missing                Terminate execution for a missing file (by default, missing files are skipped and execution continues).
        --exclude-tile, -e SELECTION      Regex matching tile names to exclude. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
        --filter-mask MASK                Run parameters override, custom pass filter mask.
        --flowcell-id FLOWCELL_ID         Run parameters override, flowcell ID.
        --force-index-orientation         Do not attempt to find orientation for I1/I2 reads (reverse complement). Use orientation given in run manifest.
        --group-fastq                     Group all FASTQ/stats/metrics for a project are in the project folder (default false)
        --help, -h                        Display this usage statement
        --i1-cycles NUM_CYCLES            Run parameters override, I1 cycles.
        --i2-cycles NUM_CYCLES            Run parameters override, I2 cycles.
        --include-tile, -i SELECTION      Regex matching tile names to include. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
        --input-remote, NAME              Rclone remote name for remote ANALYSIS_DIRECTORY
        --kit-configuration KIT_CONFIG    Run parameters override, kit configuration.
        --legacy-fastq                    Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)
        --log-level, -l LEVEL             Severity level for logging. i.e. DEBUG, INFO, WARNING, ERROR (default INFO)
        --no-error-on-invalid             Skip invalid files and continue execution (by default, execution is terminated for an invalid file).
        --no-projects                     Disable project directories (default false)
        --num-threads, -p NUMBER          Number of threads (default 1)
        --num-unassigned NUMBER           Max Number of unassigned sequences to report. (default 30)
        --output-remote, NAME             Rclone remote name for remote OUTPUT_DIRECTORY
        --preparation-workflow WORKFLOW   Run parameters override, preparation workflow.
        --qc-only                         Quickly generate run stats for single tile without generating FASTQ. Use --include-tile/--exclude-tile to define custom tile set.
        --r1-cycles NUM_CYCLES            Run parameters override, R1 cycles.
        --r2-cycles NUM_CYCLES            Run parameters override, R2 cycles.
        --run-manifest, -r PATH           Location of run manifest to use instead of default RunManifest.csv found in analysis directory
        --settings SELECTION              Run manifest settings override. This option may be specified multiple times.
        --skip-multi-qc                   Do not generate MultiQC HTML report.
        --skip-qc-report                  Do not generate HTML QC report.
        --split-lanes                     Split FASTQ files by lane
        --version, -v                     Display bases2fastq version

cyto-fastq optional arguments:
        --batch BATCH                     Restrict cyto-fastq generation to batch(es) that match comma delimited list (e.g. --batch B01,B02,B03).
        --cyto-fastq-mask MASK            Cycle mask for cyto fastq generation. This flag can be specified multiple times.
        --group-well-label                Merge FASTQ according to well label defined in run manifest (default false)
        --panel PANEL                     Local or remote path to panel JSON
        --per-target-fastq                Create per-target fastq for each cell assignment target site in each DISS batch according to FastqMasks in TargetCellAssignmentManifest.
        --tca-manifest PATH               Location of TargetCellAssignmentManifest to use instead of default csv found in analysis directory
        --well, -v                        Restrict cyto-fastq generation to well location(s) that match comma delimited list (e.g. --well A1,A2,B2)
