cloudCellphy

Nextflow pipeline for massive-scale single-cell phylogenetics

The pipeline is currently configured to run on a SLURM cluster, but can be easily adapted to other schedulers.

The basic nextflow command is:

nextflow workflows/cloudCellphy.nf

Configuration Parameters

The nextflow.config file contains various parameters that control the behavior of the pipeline. Below is an explanation of the key parameters:

Executor

• queueSize: Maximum number of jobs in the queue.
• submitRateLimit: Rate limit for job submissions.

Params

• joint_vcf: Path to the joint VCF file.
• out: Output directory.
• sample_id: Sample identifier.
• start_tree_type: Type of starting tree for CellPhy.
• evo_model: Evolutionary model for CellPhy.
• prob_msa: Enables probabilistic multiple sequence alignment.
• lh_epsilon: Likelihood epsilon value.
• n_tree_search: Number of tree searches.
• n_bootstrap_search: Number of bootstrap searches.
• bs_trees_per_job: Number of bootstrap trees per job.
• bs_metric: Metrics for bootstrap analysis.
• tree_threads: Number of threads for tree computation.
• tree_memory: Memory allocated for tree computation.

Run Time

$N$ is the number of maximum likelihood tree searches.

$t_i$ is the time to compute the $i$-th maximum likelihood tree.

$P$ is the number of workers.

Sequential execution time

$$ T_{\text{serial}} = \sum_{i=1}^{N} t_i $$

Bounded parallel execution time with P workers

$$ T_{P} \approx \frac{1}{P} \sum_{i=1}^{N} t_i + \text{tail effects} $$

Fully parallel execution time (unlimited concurrency)

$$ T_{\text{parallel}} = \max_{\substack{i=1}}^{N} t_i $$

Citation

@article{Prieto2025,
  author = {Prieto, Tamara and Yuan, Dennis J and Zinno, John and Hughes, Clayton and Midler, Nicholas and Kao, Sheng and Huuhtanen, Jani and Raviram, Ramya and Fotopoulou, Fenia and Ruthen, Neil and Rajagopalan, Srinivas and Schiffman, Joshua S and D Avino, Andrew R and Yoon, Sang-Ho and Sotelo, Jesus and Omans, Nathaniel D and Wheeler, Noelle and Garces, Alejandro and Pradhan, Barun and Cheng, Alexandre Pellan and Robine, Nicolas and Potenski, Catherine and Godfrey, Katharine and Kakiuchi, Nobuyuki and Yokoyama, Akira and Ogawa, Seishi and Abrams, Julian and Raimondi, Ivan and Landau, Dan A},
  title = {Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus},
  year = {2025},
  doi = {10.1101/2025.10.11.681805},
  journal = {bioRxiv}
}