# Research Object Crate for CHAMPAGNE: CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline

Original URL: https://workflowhub.eu/workflows/2105/ro_crate?version=1

# CHAMPAGNE 🍾 **CH**rom**A**tin i**M**muno **P**recipit**A**tion sequencin**G** a**N**alysis pip**E**line [![build](https://github.com/CCBR/CHAMPAGNE/actions/workflows/build.yml/badge.svg)](https://github.com/CCBR/CHAMPAGNE/actions/workflows/build.yml) [![docs](https://github.com/CCBR/CHAMPAGNE/actions/workflows/docs-mkdocs.yml/badge.svg)](https://ccbr.github.io/CHAMPAGNE) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10516078.svg)](https://doi.org/10.5281/zenodo.10516078) [![release](https://img.shields.io/github/v/release/CCBR/CHAMPAGNE?color=blue&label=latest%20release)](https://github.com/CCBR/CHAMPAGNE/releases/latest) View the full documentation website: CHAMPAGNE Workflow Overview. View a detailed version of the workflow diagram on the website. ## Set up Champagne is installed on the [Biowulf HPC](#biowulf). For installation in other execution environments, refer to the [docs](https://ccbr.github.io/CHAMPAGNE/). ### Biowulf Champagne is available on [Biowulf](https://hpc.nih.gov/) in the `ccbrpipeliner` module. You'll first need to start an interactive session, then load the module: ```sh # 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: ```sh # 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/$USER/champagne_project \ --mode slurm -profile test ``` To run champagne on your own data, you'll need to create a sample sheet. Take a look at these examples: - [assets/samplesheet_test.csv](https://github.com/CCBR/CHAMPAGNE/blob/main/assets/samplesheet_test.csv) - mix of single and paired end reads downloaded from github. - [assets/samplesheet_full_mm10.csv](https://github.com/CCBR/CHAMPAGNE/blob/main/assets/samplesheet_full_mm10.csv) - single end reads on biowulf. Once you've created a samplesheet with paths to your fastq files, run champagne with the `--input` option to specify the path to your sample sheet: ```sh champagne run --output /data/$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` ```YAML 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: ```sh champagne run --output /data/$USER/champagne_project \ --mode slurm \ -params-file assets/params.yml ``` View the [full list of parameters](https://ccbr.github.io/CHAMPAGNE/dev/guide/params) in the documentation. ### Reference Genomes View [the list of available reference genomes](https://ccbr.github.io/CHAMPAGNE/dev/guide/genomes) to see which genomes are pre-configured for use with champagne on biowulf. If you'd like to use a genome that's not already available, view the [guide on preparing a custom reference genome](https://ccbr.github.io/CHAMPAGNE/dev/guide/genomes/#custom-reference-genome). ### Spike-in Control If your experiment uses a spike-in control, you can specify the spike-in genome with the `--spike_genome` parameter: ```sh champagne run --output /data/$USER/champagne_project \ --mode slurm \ --input samplesheet.csv \ --genome hg38 \ --spike_genome dmelr6.32 \ --deeptools_normalize_using None ``` View [the spike-in docs](https://ccbr.github.io/CHAMPAGNE/dev/guide/spike-in/) for more information on how to use & customize spike-in controls. ## Help & Contributing Come across a **bug**? Open an [issue](https://github.com/CCBR/CHAMPAGNE/issues) and include a minimal reproducible example. Have a **question**? Ask it in [discussions](https://github.com/CCBR/CHAMPAGNE/discussions). Want to **contribute** to this project? Check out the [contributing guidelines](.github/CONTRIBUTING.md). **General Inquiries and Collaboration:** Please contact the CCBR Pipeliner team at [CCBR_Pipeliner@mail.nih.gov](mailto:CCBR_Pipeliner@mail.nih.gov). ## References This repo was originally generated from the [CCBR Nextflow Template](https://github.com/CCBR/CCBR_NextflowTemplate). The template takes inspiration from nektool[^1] 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 instructions[^2]. [^1]: nektool https://github.com/beardymcjohnface/nektool [^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core

Author
  Kelly Sovacool
License
  MIT

## Contents

Main Workflow: CHAMPAGNE: CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
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Main Workflow Diagram: docs/diagram/workflow.svg
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