This Nextflow pipeline basecalls and demultiplexes linked-reads from 10x Genomics. To run this pipeline, the 8-base sample indexes are needed, corresponding to the 10x Genomics indexes (e.g. SI-GA-A1).
This pipeline makes some assumptions about the input data. For example, it makes the assumption that it is paired-end sequencing, and therefore uses --use-bases-mask=Y*,I*,Y* in bcl2fastq, and assumes that the read lengths (and index length) is found in RunInfo.xml.
Here's how to run this pipeline on the "tiny-bcl" example dataset from 10x Genomics. First of all, download the tiny-bcl tar file and the Illumina Experiment Manager sample sheet: tiny-bcl-samplesheet-2.1.0.csv.
Download the tiny-bcl data: https://support.10xgenomics.com/genome-exome/software/pipelines/latest/using/mkfastq#example_data
Next, edit the [Data] part of the samplesheet from the following:
Lane,Sample_ID,index,Sample_Project
5,Sample1,SI-GA-C5,tiny_bcl
To the following:
Lane,Sample_ID,index
5,Sample1,CGACTTGA
5,Sample1,TACAGACT
5,Sample1,ATTGCGTG
5,Sample1,GCGTACAC
Using that the index SI-GA-C5 corresponds to the four octamers CGACTTGA,TACAGACT,ATTGCGTG,GCGTACAC. Notice that we also removed the Sample_Project column.
Provided that you've set installed all the software in environment.yml (or maybe used this pipeline's Docker container at https://hub.docker.com/r/olavurmortensen/demuxlink), you should be able to run the pipeline like this:
nextflow demuxlink/main.nf --rundir tiny-bcl-2.2.0 --outdir results --samplesheet tiny-bcl-samplesheet-2.1.0.csv
And get the FASTQ files in results/fastq_out/Sample1/outs and the FastQC reports in results/fastqc/Sample1.