elembio/bases2fastq repository overview

docker pull elembio/bases2fastq:3.0.0
docker run elembio/bases2fastq:3.0.0 bases2fastq [OPTIONS] ANALYSIS_DIRECTORY OUTPUT_DIRECTORY

Usage: bases2fastq [OPTIONS] ANALYSIS_DIRECTORY OUTPUT_DIRECTORY

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

optional arguments:
	--bgzf-compression                Use HTSlib BGZF (block compression) for FASTQ output instead of single-member gzip. Each *.fastq.gz is indexed by a corresponding `.fastq.gz.gzi` index file.
	--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                Custom pass-filter mask. For sequencing runs use read names (e.g. R1:Y10N*). For cytoprofiling runs use batch names (e.g. B01:N5Y15N*-B02:YN*). Batches not named in the mask fall back to BaseCalling/Filter/ files.
	--flowcell-id FLOWCELL_ID         Run parameters override, flowcell ID.
	--force-detect-index-orientation  Detect index orientation by scanning all tiles and using the highest-PF tile in each lane.
	--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-empty-fq-files             Do not create FASTQ files for sample/read outputs with zero reads.
	--skip-qc-report                  Do not generate the HTML QC report.
	--split-lanes                     Split FASTQ files by lane
	--unzip-to-disk                   Low-memory option: decompress bases files to temporary files on disk instead of holding them in memory (default false)
	--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.
	--segmentation PATH               Path to CellSegmentation/ directory (can be local or remote)
	--tca-manifest PATH               Location of TargetCellAssignmentManifest to use instead of default csv found in analysis directory
	--well                            Restrict cyto-fastq generation to well location(s) that match comma delimited list (e.g. --well A1,A2,B2)