Demux

A generic pipeline for running bcl2fastq, bcl-convert or Cell Ranger mkfastq.

Info

ID: demux
Namespace: workflows/ingestion

Links

Source

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

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -main-script target/nextflow/workflows/ingestion/demux/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
id: # please fill in - example: "foo"
input: # please fill in - example: "bcl_dir"
sample_sheet: # please fill in - example: "bcl_dir"
demultiplexer: "bcl2fastq"
# ignore_missing: true
# output_fastq: "$id.$key.output_fastq.output_fastq"
# output_fastqc: "$id.$key.output_fastqc.output_fastqc"
# output_multiqc: "$id.$key.output_multiqc.output_multiqc"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/ingestion/demux/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name	Description	Attributes
--id	ID of the sample.	string, required, example: "foo"
--input	Input run directory	file, required, example: "bcl_dir"
--sample_sheet	Pointer to the sample sheet	file, required, example: "bcl_dir"
--demultiplexer	The multiplexer to use, one of bclconvert or mkfastq	string, default: "bcl2fastq"
--ignore_missing	Should the demultiplexer ignore missing entities (filter, …)	boolean
--output_fastq	Output directory containig fastq files	file, required, example: "fastq_dir"
--output_fastqc	Reports directory produced by FastQC	file, example: "reports_dir"
--output_multiqc	Reports directory produced by MultiQC	file, example: "reports_dir"

Authors

• Toni Verbeiren (author, maintainer)

• Marijke Van Moerbeke (author)

• Angela Oliveira Pisco (author)

• Samuel D’Souza (author)

• Robrecht Cannoodt (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v19(cellranger_mkfastq)
    v78(mix)
    v42(bcl_convert)
    v65(bcl2fastq)
    v87(fastqc)
    v107(multiqc)
    v135(Output)
    v0-->v2
    v2-->v19
    v19-->v78
    v2-->v42
    v42-->v78
    v2-->v65
    v65-->v78
    v78-->v87
    v87-->v107
    v107-->v135
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v19 fill:#e3dcea,stroke:#7a4baa;
    style v78 fill:#e3dcea,stroke:#7a4baa;
    style v42 fill:#e3dcea,stroke:#7a4baa;
    style v65 fill:#e3dcea,stroke:#7a4baa;
    style v87 fill:#e3dcea,stroke:#7a4baa;
    style v107 fill:#e3dcea,stroke:#7a4baa;
    style v135 fill:#e3dcea,stroke:#7a4baa;