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 0.12.0 -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 0.12.0 -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
    v0(Input)
    v2(toSortedList)
    v4(flatMap)
    v5(filter)
    v10(cellranger_mkfastq)
    v12(join)
    v35(mix)
    v15(filter)
    v20(bcl_convert)
    v22(join)
    v25(filter)
    v30(bcl2fastq)
    v32(join)
    v41(fastqc)
    v43(join)
    v46(Output)
    v48(toSortedList)
    v54(multiqc)
    v56(join)
    v59(Output)
    v64(Output)
    v4-->v5
    v4-->v15
    v4-->v25
    v0-->v2
    v2-->v4
    v5-->v12
    v5-->v10
    v10-->v12
    v12-->v35
    v15-->v22
    v15-->v20
    v20-->v22
    v22-->v35
    v25-->v32
    v25-->v30
    v30-->v32
    v32-->v35
    v35-->v43
    v35-->v41
    v41-->v43
    v43-->v46
    v35-->v48
    v48-->v56
    v48-->v54
    v54-->v56
    v56-->v59
    v35-->v64