Viash Hub

Description

Demultiplexing of raw sequencing data

Input 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.

Name

Type & Properties

--id

string

--input

file

required

--run_information

file

--demultiplexer

string

Output arguments

Name	Type & Properties	Description
--output	file output	Directory to write fastq data to
--output_sample_qc	file multiple output	Directory to write FastQC output to
--multiqc_output	file output	Location where to write MultiQC output to
--output_run_information	file required output
--demultiplexer_logs	file required output

Name

Type & Properties

--output

file

output

--output_sample_qc

file

multiple

output

--multiqc_output

file

output

--output_run_information

file

required

output

--demultiplexer_logs

file

required

output

Other arguments

Name	Type & Properties	Description
--skip_copycomplete_check	boolean_true	Disable the check for the presence of a "CopyComplete.txt" file in input directory in case of Illumina data.

Name

Type & Properties

--skip_copycomplete_check

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
output: "$id.$key.output"  
output_sample_qc: "$id.$key.output_sample_qc._*"  
multiqc_output: "$id.$key.multiqc_output"  
output_run_information: "$id.$key.output_run_information"  
demultiplexer_logs: "$id.$key.demultiplexer_logs"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/demultiplex.git \  
  -revision v0.6.3 \  
  -main-script target/nextflow/demultiplex/main.nf \  
  -params-file params.yaml