A simple nextflow pipeline for obtaining Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq). The input is an Illumina run folder (with bcl files) and a SampleSheet.csv file. So far tested with runs from NextSeq and MiSeq machines. Run it with:
nextflow run angelovangel/nxf-bcl --runfolder illumina_folderThe 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 --helpI 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 amazonTip - you can then run the angelovangel/nxf-fastqc pipeline on the fastq files to get data on their quality and filter/trim them.
And finally, if you don't have nextflow go get it!
Cheers!