B/T cell repertoire analysis pipeline with immcantation framework. WIP, currently requires a bunch of changes first.
Switch branches/tags
Nothing to show
Clone or download
Pull request Compare This branch is 3 commits ahead, 4 commits behind ggabernet:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github
assets
bin
conf
docs
.gitattributes
.gitignore
.travis.yml
CHANGELOG.md
CODE_OF_CONDUCT.md
Dockerfile
LICENSE
README.md
Singularity
environment.yml
main.nf
nextflow.config
runBcellmagic.sh

README.md

nf-core/bcellmagic

A pipeline to analyze B-cell and T-cell repertoires based on Immcantation 2.5.0.

Build Status Nextflow

install with bioconda Docker Singularity Container available

Introduction

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.

Documentation

The nf-core/bcellmagic pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

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 

Credits

nf-core/bcellmagic was originally written by Gisela Gabernet, Simon Heumos and Alexander Peltzer.