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Demux
A generic pipeline for running bcl2fastq, bcl-convert or Cell Ranger mkfastq.
Info
ID: demux
Namespace: workflows/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 2.1.0 -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 2.1.0 -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" |