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 2.1.1 -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_fastqc: "$id.$key.output_fastqc"
# output_multiqc: "$id.$key.output_multiqc"

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

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -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)
    v12(filter)
    v20(cellranger_mkfastq)
    v27(cross)
    v37(cross)
    v117(mix)
    v48(filter)
    v56(bcl_convert)
    v63(cross)
    v73(cross)
    v84(filter)
    v92(bcl2fastq)
    v99(cross)
    v109(cross)
    v118(filter)
    v126(fastqc)
    v133(cross)
    v143(cross)
    v149(filter)
    v179(concat)
    v157(multiqc)
    v164(cross)
    v174(cross)
    v186(cross)
    v193(cross)
    v205(cross)
    v212(cross)
    v216(Output)
    v117-->v118
    v0-->v2
    v12-->v20
    v20-->v27
    v12-->v27
    v12-->v37
    v48-->v56
    v56-->v63
    v48-->v63
    v48-->v73
    v84-->v92
    v92-->v99
    v84-->v99
    v84-->v109
    v118-->v126
    v126-->v133
    v118-->v133
    v118-->v143
    v149-->v157
    v157-->v164
    v149-->v164
    v149-->v174
    v174-->v179
    v179-->v186
    v2-->v186
    v186-->v193
    v2-->v193
    v2-->v205
    v205-->v212
    v2-->v212
    v212-->v216
    v2-->v12
    v37-->v117
    v20-->v37
    v2-->v48
    v73-->v117
    v56-->v73
    v2-->v84
    v109-->v117
    v92-->v109
    v143-->v149
    v126-->v143
    v157-->v174
    v179-->v205
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v12 fill:#e3dcea,stroke:#7a4baa;
    style v20 fill:#e3dcea,stroke:#7a4baa;
    style v27 fill:#e3dcea,stroke:#7a4baa;
    style v37 fill:#e3dcea,stroke:#7a4baa;
    style v117 fill:#e3dcea,stroke:#7a4baa;
    style v48 fill:#e3dcea,stroke:#7a4baa;
    style v56 fill:#e3dcea,stroke:#7a4baa;
    style v63 fill:#e3dcea,stroke:#7a4baa;
    style v73 fill:#e3dcea,stroke:#7a4baa;
    style v84 fill:#e3dcea,stroke:#7a4baa;
    style v92 fill:#e3dcea,stroke:#7a4baa;
    style v99 fill:#e3dcea,stroke:#7a4baa;
    style v109 fill:#e3dcea,stroke:#7a4baa;
    style v118 fill:#e3dcea,stroke:#7a4baa;
    style v126 fill:#e3dcea,stroke:#7a4baa;
    style v133 fill:#e3dcea,stroke:#7a4baa;
    style v143 fill:#e3dcea,stroke:#7a4baa;
    style v149 fill:#e3dcea,stroke:#7a4baa;
    style v179 fill:#e3dcea,stroke:#7a4baa;
    style v157 fill:#e3dcea,stroke:#7a4baa;
    style v164 fill:#e3dcea,stroke:#7a4baa;
    style v174 fill:#e3dcea,stroke:#7a4baa;
    style v186 fill:#e3dcea,stroke:#7a4baa;
    style v193 fill:#e3dcea,stroke:#7a4baa;
    style v205 fill:#e3dcea,stroke:#7a4baa;
    style v212 fill:#e3dcea,stroke:#7a4baa;
    style v216 fill:#e3dcea,stroke:#7a4baa;