bcl_convert

demultiplex

fastq

bcl

illumina

Description

Convert bcl files to fastq files using bcl-convert.
Information about upgrading from bcl2fastq via
Upgrading from bcl2fastq to BCL Convert
and BCL Convert Compatible Products

Input arguments

Name	Type & Properties	Description
--bcl_input_directory -i	file required	Input run directory
--sample_sheet -s	file	Path to SampleSheet.csv file (default searched for in --bcl_input_directory)
--run_info	file	Path to RunInfo.xml file (default root of BCL input directory)

Name

Type & Properties

--bcl_input_directory

-i

file

required

--sample_sheet

-s

file

--run_info

file

Lane and tile settings

Name	Type & Properties	Description
--bcl_only_lane	integer	Convert only specified lane number (default all lanes)
--first_tile_only	boolean	Only convert first tile of input (for testing & debugging)
--tiles	string	Process only a subset of tiles by a regular expression
--exclude_tiles	string	Exclude set of tiles by a regular expression

Name

Type & Properties

--bcl_only_lane

integer

--first_tile_only

boolean

--tiles

string

--exclude_tiles

string

Resource arguments

Name	Type & Properties	Description
--shared_thread_odirect_output	boolean	Use linux native asynchronous io (io_submit) for file output (Default=false)
--bcl_num_parallel_tiles	integer	\# of tiles to process in parallel (default 1)
--bcl_num_conversion_threads	integer	\# of threads for conversion (per tile, default # cpu threads)
--bcl_num_compression_threads	integer	\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)
--bcl_num_decompression_threads	integer	\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8). Only applies when preloading files

Name

Type & Properties

--shared_thread_odirect_output

boolean

--bcl_num_parallel_tiles

integer

--bcl_num_conversion_threads

integer

--bcl_num_compression_threads

integer

--bcl_num_decompression_threads

integer

Run arguments

Name	Type & Properties	Description
--bcl_only_matched_reads	boolean	For pure BCL conversion, do not output files for 'Undetermined' [unmatched] reads (output by default)
--no_lane_splitting	boolean	Do not split FASTQ file by lane (false by default)
--num_unknown_barcodes_reported	integer	\# of Top Unknown Barcodes to output (1000 by default)
--bcl_validate_sample_sheet_only	boolean	Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)
--strict_mode	boolean	Abort if any files are missing (false by default)
--sample_name_column_enabled	boolean	Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories

Name

Type & Properties

--bcl_only_matched_reads

boolean

--no_lane_splitting

boolean

--num_unknown_barcodes_reported

integer

--bcl_validate_sample_sheet_only

boolean

--strict_mode

boolean

--sample_name_column_enabled

boolean

Output arguments

Name	Type & Properties	Description
--output_directory -o	file required output	Output directory containig fastq files
--bcl_sampleproject_subdirectories	boolean	Output to subdirectories based upon sample sheet 'Sample_Project' column
--fastq_gzip_compression_level	integer	Set fastq output compression level 0-9 (default 1)
--reports	file output	Reports directory
--logs	file output	Reports directory
--force	boolean	Allow destination directory to already exist and overwrite files.

Name

Type & Properties

--output_directory

-o

file

required

output

--bcl_sampleproject_subdirectories

boolean

--fastq_gzip_compression_level

integer

--reports

file

output

--logs

file

output

--force

boolean

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"  
reports: "$id.$key.reports.reports_dir"  
logs: "$id.$key.logs.logs_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bcl_convert/main.nf \  
  -params-file params.yaml

bcl_convert

Input arguments

Lane and tile settings

Resource arguments

Run arguments

Output arguments

Run this component

Relationships

Used by

Uses