detect_demultiplexer

Description

Detects the demultiplexer and accompanying sample information file which can be
used to generate the fastq files.

Type

nextflow_script

License

MIT

Links

Repository

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
demultiplexer_output: "$id.$key.demultiplexer_output"  
run_information_output: "$id.$key.run_information_output"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/demultiplex.git \  
  -revision v0.6.1 \  
  -main-script target/nextflow/detect_demultiplexer/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--id	string	Unique identifier for the run
--input	file required	Directory containing raw sequencing data
--run_information	file	CSV file containing sample information, which will be used as input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina) or 'RunManifest.csv' (Element Biosciences). If not specified, will try to autodetect the sample sheet in the input directory. Requires --demultiplexer to be set.
--demultiplexer	string	Demultiplexer to use, choice depends on the provider of the instrument that was used to generate the data. When not using --sample_sheet, specifying this argument is not required.
--demultiplexer_output	string output	Demultiplexer program. The demultiplexer is either provided (with --demultiplexer), or inferred from the contents of the input data.
--run_information_output	file output	Sample information that can be used to demultiplex the input data. An appropriate file was either provided (with --run_information), or inferred from the contents of the input data.

Name

Type & Properties

--id

string

--input

file

required

--run_information

file

--demultiplexer

string

--demultiplexer_output

string

output

--run_information_output

file

output