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nf-core/bcl2fastq @ 0.0.0-3fc6d40

Demultiplex Illumina BCL files

demultiplex illumina fastq
Latest version: 0.0.0-3fc6d40
Total downloads: 7
Source: nf-core/modules
Authors: @matthdsm
Maintainers: @matthdsm

Updating the docker container and making a new module release

bcl2fastq is a commercial tool from Illumina. The container provided for the bcl2fastq nf-core module is not provided nor supported by Illumina. Updating the bcl2fastq versions in the container and pushing the update to Dockerhub needs to be done manually.

  1. Navigate to the appropriate download page. - bcl2fastq: download the rpm of the desired bcl2fastq version with curl or wget.

  2. Unpack the RPM package using rpm2cpio bcl2fastq2-*.rpm | cpio -i --make-directories.

    • Move the executable located in <unpack_dir>/usr/bin/bcl2fastq into the same folder as the Dockerfile.
    • Move the css and xsl directories from <unpack_dir>/local/share/ into the same folder as the Dockerfile

  3. Create and test the container:

    docker build . -t nfcore/bcl2fastq:<VERSION>

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

    docker push nfcore/bcl2fastq:<VERSION>
Process
Name BCL2FASTQ
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 9 channels
#1 xml tuple
meta map

Groovy Map containing sample information
**/*.xml file

Output XML files, for example RunInfo.xml

 **/*.xml
#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 stats tuple
meta map

Groovy Map containing sample information
output/Stats file

Statistics files

 Stats
#4 interop tuple
meta map

Groovy Map containing sample information
InterOp/*.bin file

Interop files

 *.{bin}
#5 reports tuple
meta map

Groovy Map containing sample information
output/Reports file

Demultiplexing Reports

 Reports
#6 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
#7 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
#8 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
#9 versions_bcl2fastq tuple
${task.process} string

The name of the process
bcl2fastq string

The name of the tool
bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//' eval

The expression to obtain the version of the tool
Tool Description Homepage
bcl2fastq Demultiplex Illumina BCL files https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software
Version 0.0.0-3fc6d40
Commit ID