angelovangel/nxf-bcl

A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)

nxf-bcl

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

nxf-bcl's Issues

output sample sheet in results

would be nice to have the sample sheet used for bcl2fastq in the results folder

add parameter for number of allowed mismatches per index

--barcode-mismatches arg (=1)                   number of allowed mismatches per index
                                                  Multiple, comma delimited, entries allowed. Each entry is applied to the corresponding index; last entry applies to all
                                                  remaining indices.
                                                  Accepted values: 0, 1, 2.

Switch to BCL Convert

Migrate the pipeline from bcl2fastq to BCL Convert, see bulletin

Output excel file with clusters per sample

nextflow report should be output by default

for documentation purposes, make --with report a default