Bcl convert

Convert bcl files to fastq files using bcl-convert.


ID: bcl_convert
Namespace: demux

Information about upgrading from bcl2fastq via https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html

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 0.12.6 -latest \
  -main-script target/nextflow/demux/bcl_convert/main.nf \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "bcl_dir"
sample_sheet: # please fill in - example: "bcl_dir"
# output: "$id.$key.output.output"
# reports: "$id.$key.reports.reports"
test_mode: false

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/demux/bcl_convert/main.nf \
  -params-file params.yaml

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group


Name Description Attributes
--input Input run directory file, required, example: "bcl_dir"
--sample_sheet Pointer to the sample sheet file, required, example: "bcl_dir"
--output Output directory containig fastq files file, required, example: "fastq_dir"
--reports Reports directory file, example: "reports_dir"
--test_mode Should bcl-convert be run in test mode (using –first-tile-only)? boolean, default: FALSE


  • Toni Verbeiren (author, maintainer)

  • Marijke Van Moerbeke (author)