Bcl2fastq

Convert bcl files to fastq files using bcl2fastq

Info

ID: bcl2fastq
Namespace: demux

Links

Source

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/demux/bcl2fastq/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "bcl_dir"
sample_sheet: # please fill in - example: "SampleSheet.csv"
# output: "$id.$key.output"
# reports: "$id.$key.reports"
ignore_missing: false

# 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/demux/bcl2fastq/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
--input	Input run directory	file, required, example: "bcl_dir"
--sample_sheet	Pointer to the sample sheet	file, required, example: "SampleSheet.csv"
--output	Output directory containig fastq files	file, required, example: "fastq_dir"
--reports	Reports directory	file, example: "reports_dir"
--ignore_missing		boolean_true

Authors

• Toni Verbeiren (author, maintainer)