MiXCR: a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data
https://github.com/milaboratory/mixcr/
https://mixcr.readthedocs.io/en/master/index.html
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>
Use the following command to run the pipeline:
nextflow run \
main.nf \
-profile slurm,conda \
-N [email protected] \
--outdir ./outdir \
--samplesheet <path>/<samplesheet>.csv \
--email [email protected] \
--partition sahmri_prod_hpc