workflows/ingestion/demux
Description
Convert .bcl files to .fastq files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--id | string required | ID of the sample. |
--input -i | file required | Directory containing BCL files |
--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 |
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 v4.2.0 \
-main-script target/nextflow/workflows/ingestion/demux/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/ingestion/demuxopenpipeline v4.2.0