Demux
A generic pipeline for running bcl2fastq, bcl-convert or Cell Ranger mkfastq.
Info
ID: demux
Namespace: ingestion
Links
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 |
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