Demux

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

Info

ID: demux
Namespace: 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 0.10.0 -latest \
  -main-script ./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

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

nextflow run openpipelines-bio/openpipeline \
  -r 0.10.0 -latest \
  -profile docker \
  -main-script ./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

Authors

• Toni Verbeiren (author, maintainer)

• Marijke Van Moerbeke (author)

• Angela Oliveira Pisco (author)

• Samuel D’Souza (author)

• Robrecht Cannoodt (author)

Visualisation

flowchart LR
    p0(Input)
    p2(toSortedList)
    p4(flatMap)
    p5(filter)
    p10(cellranger_mkfastq)
    p12(join)
    p35(mix)
    p15(filter)
    p20(bcl_convert)
    p22(join)
    p25(filter)
    p30(bcl2fastq)
    p32(join)
    p41(fastqc)
    p43(join)
    p46(Output)
    p48(toSortedList)
    p54(multiqc)
    p56(join)
    p59(Output)
    p63(Output)
    p4-->p5
    p4-->p15
    p4-->p25
    p0-->p2
    p2-->p4
    p5-->p12
    p5-->p10
    p10-->p12
    p12-->p35
    p15-->p22
    p15-->p20
    p20-->p22
    p22-->p35
    p25-->p32
    p25-->p30
    p30-->p32
    p32-->p35
    p35-->p43
    p35-->p41
    p41-->p43
    p43-->p46
    p35-->p48
    p48-->p56
    p48-->p54
    p54-->p56
    p56-->p59
    p35-->p63