
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). Also set by --strict.
        --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). Overridden by --strict options.
        --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. Must be <= 1000 (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-qc-report SELECTION      Do not generate HTML QC report.
        --split-lanes                   Split FASTQ files by lane
        --strict, -s                    In strict mode any invalid or missing input file will terminate execution (overrides no-error-on-invalid and sets --error-on-missing)
        --version, -v                   Display bases2fastq version