CHAMPAGNE 🍾

CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

View the full documentation website: https://ccbr.github.io/CHAMPAGNE

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, then load the module:

# start an interactive node
sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200

# load the ccbrpipeliner module
module load ccbrpipeliner

Quickstart

Initialize and run champagne with test data:

# copy the champagne config files to your project directory.
# --output is optional and defaults to your current working directory.
champagne init --output /data/$USER/champagne_project

# preview the champagne jobs that will run with the test dataset
champagne run --output /data/$USER/champagne_project \
  --mode local -profile test -preview

# launch a champagne run on slurm with the test dataset
champagne run --output /data/$USER/champagne_project \
  --mode slurm -profile test

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_full_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 --output /data/$USER/champagne_project \
    --mode slurm \
    --input samplesheet.csv \
    --genome hg38

Parameters

You can specify workflow parameters via the command line or in a YAML file. Here's an example YAML file with some common parameters:

assets/params.yml

input: './assets/samplesheet_full_mm10.csv'
contrasts: './assets/contrasts_full_mm10.csv'
genome: mm10
run_gem: false
run_chipseeker: false
run_qc: true

You can then use these parameters with the -params-file option:

champagne run --output /data/$USER/champagne_project \
    --mode slurm \
    -params-file assets/params.yml

View the full list of parameters in the documentation.

Reference Genomes

View the list of available reference genomes to see which genomes are pre-configured for use with champagne on biowulf. If you'd like to use a genome that's not already available, view the guide on preparing a custom reference genome.

Spike-in Control

If your experiment uses a spike-in control, you can specify the spike-in genome with the --spike_genome parameter:

champagne run --output /data/$USER/champagne_project \
    --mode slurm \
    --input samplesheet.csv \
    --genome hg38 \
    --spike_genome dmelr6.32 \
    --deeptools_normalize_using None

View the spike-in docs for more information on how to use & customize spike-in controls.

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.

General Inquiries and Collaboration: Please contact the CCBR Pipeliner team at [email protected].

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 ↩