bases2fastq

demultiplex

fastq

demux

Element Biosciences

Description

Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.

Type

bash_script

License

Proprietary

Keywords

demultiplex

fastq

demux

Element Biosciences

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_directory: "$id.$key.output_directory.fastq_dir"  
report: "$id.$key.report"  
logs: "$id.$key.logs.logs_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bases2fastq/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--analysis_directory	file required	Location of analysis directory
--run_manifest -r	file	Location of run manifest to use instead of default RunManifest.csv found in analysis directory

Name

Type & Properties

--analysis_directory

file

required

--run_manifest

-r

file

Output

Name	Type & Properties	Description
--output_directory -o	file required output	Location to save output fastqs
--report	file output	Output location for the HTML report
--logs	file output	Directory containing log files

Name

Type & Properties

--output_directory

-o

file

required

output

--report

file

output

--logs

file

output

Arguments

Name	Type & Properties	Description
--chemistry_version	string	Run parameters override, chemistry version.
--demux_only -d	boolean_true	Generate demux files and indexing stats without generating FASTQ
--detect_adapters	boolean_true	Detect adapters sequences, overriding any sequences present in run manifest.
--error_on_missing	boolean_true	Terminate execution for a missing file (by default, missing files are skipped and execution continues). Also set by --strict.
--exclude_tile -e	string multiple	Regex matching tile names to exclude. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
--filter_mask	string	Run parameters override, custom pass filter mask.
--flowcell_id	string	Run parameters override, flowcell ID.
--force_index_orientation	boolean_true	Do not attempt to find orientation for I1/I2 reads (reverse complement). Use orientation given in run manifest.
--group_fastq	boolean_true	Group all FASTQ/stats/metrics for a project are in the project folder.
--i1_cycles	integer	Run parameters override, I1 cycles.
--i2_cycles	integer	Run parameters override, I2 cycles
--include_tile -i	string multiple	Regex matching tile names to include. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)
--kit_configuration	string	Run parameters override, kit configuration.
--legacy_fastq	boolean_true	Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)
--log_level -l	string	Severity level for logging.
--no_error_on_invalid	boolean_true	Skip invalid files and continue execution. Overridden by --strict options
--no_projects	boolean_true	Disable project directories
--num_unassigned	integer	Max Number of unassigned sequences to report.
--preparation_workflow	string	Run parameters override, preparation workflow.
--qc_only	boolean_true	Quickly generate run stats for single tile without generating FASTQ. Use --include_tile/--exclude_tile to define custom tile set.
--r1_cycles	integer	Run parameters override, R1 cycles.
--r2_cycles	integer	Run parameters override, R2 cycles.
--split_lanes	boolean_true	Split FASTQ files by lane.
--skip_qc_report	boolean_true	Do not generate HTML QC report.
--skip_multi_qc	boolean_true	Do not generate MultiQC HTML report.
--settings	string multiple	Run manifest settings override. This option may be specified multiple times.

Name

Type & Properties

--chemistry_version

string

--demux_only

-d

boolean_true

--detect_adapters

boolean_true

--error_on_missing

boolean_true

--exclude_tile

-e

string

multiple

--filter_mask

string

--flowcell_id

string

--force_index_orientation

boolean_true

--group_fastq

boolean_true

--i1_cycles

integer

--i2_cycles

integer

--include_tile

-i

string

multiple

--kit_configuration

string

--legacy_fastq

boolean_true

--log_level

-l

string

--no_error_on_invalid

boolean_true

--no_projects

boolean_true

--num_unassigned

integer

--preparation_workflow

string

--qc_only

boolean_true

--r1_cycles

integer

--r2_cycles

integer

--split_lanes

boolean_true

--skip_qc_report

boolean_true

--skip_multi_qc

boolean_true

--settings

string

multiple

Cyto-fastq Arguments

Name	Type & Properties	Description
--batch	string	Restrict cyto-fastq generation to batch(es) that match comma delimited list (e.g. --batch B01,B02,B03).
--cyto_fastq_mask	string multiple	Cycle mask for cyto fastq generation. This flag can be specified multiple times.
--group_well_label	boolean_true	Merge FASTQ according to well label defined in run manifest.
--panel	file	Local or remote path to panel JSON
--per_target_fastq	boolean_true	Create per-target fastq for each cell assignment target site in each DISS batch according to FastqMasks in TargetCellAssignmentManifest.
--tca_manifest	file	Location of TargetCellAssignmentManifest to use instead of default csv found in analysis directory

Name

Type & Properties

--batch

string

--cyto_fastq_mask

string

multiple

--group_well_label

boolean_true

--panel

file

--per_target_fastq

boolean_true

--tca_manifest

file