A pipeline to analyze B-cell and T-cell repertoires based on Immcantation 2.5.0.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The nf-core/bcellmagic pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
Input needs to be a TSV file following this format in general:
ID Source Treatment Extraction_time Population R1 R2 I1 QMKMK072AD Patient 2 Terifluomid baseline p sample_S8_L001_R1_001.fastq.gz sample_S8_L001_R2_001.fastq.gz sample_S8_L001_I1_001.fastq.gz
Attention, the R1/R2 and I1 naming patterns are crucial!
An example call of the pipeline could be then:
nextflow run ggabernet/bcellmagic -profile standard,docker --metadata metasheet_test.tsv --cprimers CPrimers_IG.fasta --vprimers VPrimers.fasta --max_memory 8.GB --max_cpus 8 -resume
nf-core/bcellmagic was originally written by Gisela Gabernet, Simon Heumos and Alexander Peltzer.