CHAMPAGNE 🍾

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

🚧 This project is under active development. It is not yet ready for production use. 🚧

Set up

Champagne is installed on the Biowulf HPC. For installation in other execution environments, refer to the docs.

Biowulf

Champagne is available on Biowulf in the ccbrpipeliner module. You'll first need to start an interactive session and create a directory from where you'll run champagne.

# start an interactive node
sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200
# make a working directory for your project and go to it
mkdir -p /data/$USER/chipseq
cd /data/$USER/chipseq
# load the ccbrpipeliener module
module load ccbrpipeliner

Usage

Initialize and run champagne with test data:

# copy the champagne config files to your current directory
champagne init
# preview the champagne jobs that will run with the test dataset
champagne run --mode local -profile test -preview
# launch a champagne run on slurm with the test dataset
champagne run --mode slurm -profile test,biowulf

To run champagne on your own data, you'll need to create a sample sheet. Take a look at these examples:

• assets/samplesheet_test.csv - mix of single and paired end reads downloaded from github.
• assets/samplesheet_mm10.csv - single end reads on biowulf.

Once you've created a samplesheet with paths to your fastq files, run champagne with the --input option to specify the path to your sample sheet:

champagne run --mode slurm -profile biowulf --input samplesheet.csv --genome hg38

We currently support the hg38 and mm10 genomes. If you'd like to use a custom genome, you'll need the following files:

• genome fasta
• genome GTF
• blacklist fasta

Prepare your custom reference genome with:

champagne run --mode slurm -profile biowulf \
    -entry MAKE_REFERENCE \
    --outdir custom_genome \
    --genome custom_genome \
    --genome_fasta genome.fasta \
    --genes_gtf genome.gtf \
    --blacklist blacklist.fasta

The reference files and a config file for the genome will be written in custom_genome/genome.

Then you can run champagne using your custom genome:

champagne run --mode slurm -profile biowulf \
    --input samplesheet.csv \
    --genome custom_genome \
    -c custom_genome/genome/custom_genome.config

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

References

This repo was originally generated from the CCBR Nextflow Template. The template takes inspiration from nektool¹ and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow nf-core's instructions².

Footnotes

1. nektool https://github.com/beardymcjohnface/nektool ↩

2. instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core ↩