Bcl convert

Convert bcl files to fastq files using bcl-convert.

Info

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 2.1.0 -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"
# reports: "$id.$key.reports"
test_mode: false
strict_mode: false
# tiles: "foo"
# exclude_tiles: "foo"
# no_lane_splitting: true

# 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/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
--strict_mode Abort if any files are missing. boolean, default: FALSE
--tiles Process only a subset of tiles by a regular expression. string
--exclude_tiles Exclude set of tiles by a regular expression string
--no_lane_splitting Wheter to avoid splitting FASTQ file by lane. boolean

Authors

  • Toni Verbeiren (author, maintainer)

  • Marijke Van Moerbeke (author)

  • Weiwei Schultz (contributor)

  • Dorien Roosen (author)