iCLIP

An RNA Biology pipeline to characterize protein-RNA interactions.

1. Getting Started!

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (tba later!).

1.1 Download the workflow

Please clone this repository to your local filesystem using the following command:

# Clone Repository from Github
git clone https://github.com/RBL-NCI/iCLIP.git
# Change your working directory to the iCLIP repo
cd iCLIP/

1.2 Add snakemake to PATH

Please make sure that snakemake>=5.19 is in your $PATH. If you are in Biowulf, please load the following environment module:

# Recommend running snakemake>=5.19
module load snakemake/5.24.1

1.3 Configure workflow

Configure the workflow according to your needs via editing the files in the config/ folder. Adjust snakemake_config.yaml to configure the workflow execution and cluster_config.yml to configure the cluster settings. Create multiplex.tsv and samples.tsv files to specify your sample setup, or edit the example manifests in the manifest/ folder.

1.4 Dry-run the workflow

Run the following command to dry-run the snakemake pipeline:

sh run_snakemake.sh dry-run

Review the log to ensure there are no workflow errors.

2. Usage

Submit master job to the cluster:

sh run_snakemake.sh cluster

Submit master job locally:

sh run_snakemake.sh local

3. Contribute

This section is for new developers working with the iCLIP pipeline. If you have added new features or adding new changes, please consider contributing them back to the original repository:

1. Fork the original repo to a personal or org account.
2. Clone the fork to your local filesystem.
3. Copy the modified files to the cloned fork.
4. Commit and push your changes to your fork.
5. Create a pull request to this repository.