Viash Hub

Description

Convert bcl files to fastq files using bcl2fastq.

Arguments

Name	Type & Properties	Description
--input -i --runfolder_dir	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
--ignore_missing	boolean_true	Interpret missing .bcl files as no call (N), interpret missing control files as not-set control bits and fill in with zeros when .stats files are missing.

Name

Type & Properties

--input

-i

--runfolder_dir

file

required

--sample_sheet

-s

file

required

--output

-o

file

required

output

--reports

file

output

--ignore_missing

boolean_true

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"  
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/bcl2fastq/main.nf \  
  -params-file params.yaml

Relationships

Used by

1 relationships

workflows/ingestion/demuxopenpipeline v4.2.0

Current component

demux/bcl2fastqopenpipeline v4.2.0

Uses

0 relationships

No component dependencies found.