Bcl convert

Convert bcl files to fastq files using bcl-convert.

Info

ID: bcl_convert
Namespace: demux

Links

Source

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

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 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/demux/bcl_convert/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: "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

Authors

• Toni Verbeiren (author, maintainer)

• Marijke Van Moerbeke (author)