workflows/ingestion/demux

Description

Convert .bcl files to .fastq files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.

Type

nextflow_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
demultiplexer: [ "bcl2fastq" ]  
output_fastq: "$id.$key.output_fastq.fastq_dir"  
output_fastqc: "$id.$key.output_fastqc.reports_dir"  
output_multiqc: "$id.$key.output_multiqc.reports_dir"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.0 \  
  -main-script target/nextflow/workflows/ingestion/demux/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input -i	file required	Input run directory
--sample_sheet -s	file required	Pointer to the sample sheet
--demultiplexer	string	The multiplexer to use, one of bclconvert or mkfastq
--ignore_missing	boolean	Should the demultiplexer ignore missing entities (filter, ...)
--output_fastq	file required output	Output directory containig fastq files
--output_fastqc	file output	Reports directory produced by FastQC
--output_multiqc	file output	Reports directory produced by MultiQC

Name

Type & Properties

--id

string

required

--input

-i

file

required

--sample_sheet

-s

file

required

--demultiplexer

string

--ignore_missing

boolean

--output_fastq

file

required

output

--output_fastqc

file

output

--output_multiqc

file

output