demux/bcl_convert

Description

Convert bcl files to fastq files using bcl-convert.
Information about upgrading from bcl2fastq via
https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html
and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.fastq_dir"  
reports: "$id.$key.reports.reports_dir"  
test_mode: [ false ]  
strict_mode: [ false ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/demux/bcl_convert/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input run directory
--sample_sheet -s	file required	Pointer to the sample sheet
--output -o	file required output	Output directory containig fastq files
--reports	file output	Reports directory
--test_mode	boolean	Should bcl-convert be run in test mode (using --first-tile-only)?
--strict_mode	boolean	Abort if any files are missing.
--tiles	string	Process only a subset of tiles by a regular expression.
--exclude_tiles	string	Exclude set of tiles by a regular expression
--no_lane_splitting	boolean	Wheter to avoid splitting FASTQ file by lane.

Name

Type & Properties

--input

-i

file

required

--sample_sheet

-s

file

required

--output

-o

file

required

output

--reports

file

output

--test_mode

boolean

--strict_mode

boolean

--tiles

string

--exclude_tiles

string

--no_lane_splitting

boolean