MiXCR Pipeline

MiXCR: a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

https://mixcr.readthedocs.io/en/master/index.html

Usage

1. Create a Sample-sheet

The sample-sheet is a CSV file of the following structure:

path,group,sample,filename,R1,R2
<path>,GROUP,TEST-0001,TEST-0001-XT,TEST-0001-XT_1.fastq.gz,TEST-0001-XT_2.fastq.gz

The columns are as follows:

path = Path to parent directory of all ALL Fastq files
group = Age group that sample belongs to e.g. AYAII
sample = Sample identifier e.g. AYAII_0001
filename = Fastq file basename e.g. AYAII-0001-DIA1-PB
R1/R2 = Fastq filename (e.g AYAII-0001-DIA1-PB_R1.fastq.gz)

The group and sample values are actually sub directories of path. The pipeline gets samples by building the following path internally:

|--------------- path --------------| |-group-|  |--sample--|
/cancer/storage/raw_fastq/ALL/RNAseq/   AYAII/   AYAII_0001/   <fastq reads at this level>

2. Run the Pipeline

Use the following command to run the pipeline:

nextflow run \
    main.nf \
    -profile slurm,conda \
    -N email@gmail.com \
    --outdir ./outdir \
    --samplesheet <path>/<samplesheet>.csv \
    --email email@gmail.com \
    --partition sahmri_prod_hpc

ashleethomson/Nextflow_MiXCR

MiXCR Pipeline

Usage

1. Create a Sample-sheet

2. Run the Pipeline