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nf-core/bclconvert @ 0.0.0-3fc6d40

Demultiplex Illumina BCL files

demultiplex illumina fastq
Latest version: 0.0.0-3fc6d40
Total downloads: 8
Source: nf-core/modules
Authors: @matthdsm
Maintainers: @matthdsm @maxulysse

Updating the docker container and making a new module release

bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually.

  1. Navigate to the appropriate download page. - BCL Convert: find and download the latest version of bcl-convert RPM package.

  2. Update the BCL_VERSION in the Dockerfile

  3. Create and test the container:

    docker build . -t quay.io/nf-core/bclconvert:<VERSION>

  4. Access rights are needed to push the container to the Dockerhub nf-core organization, please ask a core team member to do so.

    docker push quay.io/nf-core/bclconvert:<VERSION>
Process
Name BCLCONVERT
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
samplesheet file

Input samplesheet

 *.{csv}
run_dir file

Input run directory containing RunInfo.xml and BCL data Could be a directory or a tar of the directory
Output 8 channels
#1 logs tuple
meta map

Groovy Map containing sample information
output/Logs file

Demultiplexing Logs

 Logs
#2 fastq tuple
meta map

Groovy Map containing sample information
output/**_S[1-9]*_R?_00?.fastq.gz file

Demultiplexed sample FASTQ files

 **_S*_L00?_R?_00?.fastq.gz
#3 interop tuple
meta map

Groovy Map containing sample information
output/InterOp/*.bin file

Interop files

 InterOp/*.bin
#4 reports tuple
meta map

Groovy Map containing sample information
output/Reports file

Demultiplexing Reports

 Reports
#5 fastq_idx tuple
meta map

Groovy Map containing sample information
output/**_S[1-9]*_I?_00?.fastq.gz file

Optional demultiplexed index FASTQ files

 **_S*_L00?_I?_00?.fastq.gz
#6 undetermined tuple
meta map

Groovy Map containing sample information
output/**Undetermined_S0*_R?_00?.fastq.gz file

Optional undetermined sample FASTQ files

 Undetermined_S0_L00?_R?_00?.fastq.gz
#7 undetermined_idx tuple
meta map

Groovy Map containing sample information
output/**Undetermined_S0*_I?_00?.fastq.gz file

Optional undetermined index FASTQ files

 Undetermined_S0_L00?_I?_00?.fastq.gz
#8 versions_bclconvert tuple
${task.process} string

The name of the process
bclconvert string

The name of the tool
bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //' eval

The expression to obtain the version of the tool
Tool Description Homepage
bclconvert Demultiplex Illumina BCL files https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html
Version 0.0.0-3fc6d40
Commit ID 3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date 22 Apr 2026 15:03:25 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fbclconvert/0.0.0-3fc6d40/download