detect_demultiplexer
Description
Detects the demultiplexer and accompanying sample information file which can be
used to generate the fastq files.
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. |
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 v0.6.2 \
-main-script target/nextflow/detect_demultiplexer/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
detect_demultiplexerdemultiplex v0.6.2
Uses
0 relationships
No component dependencies found.