cfClone-smk

A Snakemake pipeline for running cfClone.

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Important

Pipeline requires snakemake v9.4 or greater

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Dependencies

• conda, version >24.7.1
• Snakemake, version >=9.4

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Setup

This pipeline requires that conda and Snakemake be installed; the Bioconda package channel must also be configured.

Environment Setup

1. Ensure that you have a working conda installation, you can do this by installing Miniforge.
2. Configure the Bioconda channel and set strict channel priority:

   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   

3. Install Snakemake:

   conda create -c conda-forge -c bioconda --name snakemake snakemake'>=9.4'
   

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Usage

1. Adjust the configuration file to suit your dataset.
2. The following fields are required:
   • out_dir: path the output directory
   • clonal_cn_bed: path to the input (phased) clonal copy number profiles, in .bed format
   • clone_tree_newick: path to the clone phylogenetic tree, in newick (.nwk) format
   • sample_tsv: Path to bulk sample paths .tsv file, must contain the following columns:
     • sample_id: populated with sample IDs
     • path: populated with fully resolved paths to the input bulk sample data files
3. For a full description of all available pipeline options, please refer to the schema
4. The remaining configuration options have been named to mirror the options cfClone, to read more on the available options and their use cases:
   • cfClone documentation

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Slurm Cluster Support

A slurm workflow-profile has been created: here

Adjust as needed.

To run this pipeline using the slurm workflow-profile:

1. Ensure that the required snakemake plugins are installed.
2. SSH onto the cluster
3. On the login node start a screen session:
   • screen -S cfclone
4. From the screen session, activate your snakemake conda environment:
   • conda activate snakemake
5. From the screen session, launch the pipeline using the slurm workflow-profile:
   • snakemake --workflow-profile profiles/slurm --configfile <path/to/config-file>

Tip

Might be a good idea to launch a dry-run of the pipeline to ensure the ruleset and output are as you expect: snakemake --workflow-profile profiles/slurm -n -q rules

Required Snakemake Plugins for Slurm Cluster Support

Please ensure the following plugin is available in your snakemake conda environment:

• Slurm Plugin

The plugin is available through the Bioconda package channel:

• Slurm Plugin
• conda install snakemake-executor-plugin-slurm

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Workflow Rulegraph