A simple nextflow pipeline for obtaining Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq) from Illumina raw data. The input is an Illumina run folder (with bcl files) and a SampleSheet.csv file. The pipeline has been tested with runs from all Illumina machines. Run it with:

nextflow run angelovangel/nxf-bcl --runfolder illumina_folder

The pipeline runs in a docker container by default, so no need to install anything (except nextflow of course). It executes the Illumina programs InterOp summary and bcl2fastq, saves the fastq files in results-bcl/fastq/, and generates a MultiQC report in results-bcl/. That's it!

The above command assumes SampleSheet.csv is in the Illumina runs folder. Using the --samplesheet parameter, a different sample sheet can be passed. For all available parameters, try

nextflow run angelovangel/nxf-bcl --help

I have uploaded a small test dataset from Illumina on Amazon S3, to run the pipeline with it use:

nextflow run angelovangel/nxf-bcl -profile test
# might take some time to get the data from amazon

Tip - For generating the required sample sheet you can use the sample sheet generator app, and for analysis of the generated fastq files you can run the angelovangel/nxf-fastqc pipeline.

And finally, if you don't have nextflow go get it!
Cheers!

Update 08-01-2023

Use nextflow run -dsl1 ..., the pipeline is still using DSL1 syntax