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bihealth / digestiflow-demux

:spaghetti: Digestiflow Demultiplexing Tool
MIT License
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Investigate Illumina's BCLConvert #33

Open messersc opened 2 years ago

messersc commented 2 years ago

https://blog.software.illumina.com/2020/07/30/announcing-the-release-of-bcl-convert-software/

messersc commented 2 years ago

See https://support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html for an overview of what changed from bcl2fastq2 to BCLConvert.

One big change is that they moved from command line options to specifying parameters in a special section of the sample sheet, so we would need a new writer for that.

messersc commented 2 years ago

Looks like BCLconvert is only available for CentOS 7, so we might need to use a solution based on Docker/Singularity.

https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html

holtgrewe commented 2 years ago

I strongly support wrapping this in a singularity image as we are trying to keep the set of software maintained by HPC IT small. With singularity, updates can be rolled out at any time without administration intervention.

messersc commented 2 years ago

Have written confirmation from Illumina Tech support that they will only support CentOS.

Singularity build instructions example here: https://gist.github.com/pansapiens/f66bdb59230004eba0d7fdec9e7eb5d8