spi-nf: The SCRaMbLE Polymer Interaction model (SPI) workflow

Overview

SPI is a statical mechanics model to conduct \acrshort{scramble} experiments in silico. SPI uses polymer physics to model recombinations between loxpSym sites, and implements efficient rejection sampling and histogram reweighting algorithms to study synthetic genome evolution properties.

Configuration

• name: mnemonic name of the run (default: spi)
• outdir: basedir for storing results (default: results/)
• genome.structure: genome structure file (default: syn9r_structure.txt, bundled)
• genome.reconstruction: genome reconstruction file (default: syn9r_reconstructions.txt, bundled)
• model.lambda: list of lambda parameters for the model (default: [4,5])
• model.nu: list of nu parameters for the model (default: [0.3,0.4])
• model.configs: maximum number of genome configurations (samples) to generate (default: 10)
• model.reweight.run =
  • yes : runs reweighting right after rejection sampling
  • only : runs reweighting only and requires a trajectories file that must be specified by the paramter model.reweight.trajectories
  • no : skips reweighting.
• model.reweight.lambda: list of lambda parameters for histogram reweighting.
• model.reweight.nu: list of nu parameters for histogram reweighting.
• model.reweight.b : list of b parameters for histogram reweighting.
• model.reweight.lambda_radius: select trajectories within lambda_radius from the reweighted parameter.
• model.reweight.nu_radius : select trajectories within nu_radius from the reweighted parameter.
• model.reweight.b_radius : select trajectories within b_radius from the reweighted parameter.

Running the workflow

Install or update the workflow

nextflow pull stracquadaniolab/spi-nf

Run the analysis

nextflow run stracquadaniolab/spi-nf

Run the analysis with singularity on a slurm cluster

nextflow run stracquadaniolab/spi-nf -profile slurm,singularity

Run the analysis with docker on a slurm cluster

nextflow run stracquadaniolab/spi-nf -profile docker,singularity

Run the analysis with docker locally

nextflow run stracquadaniolab/spi-nf -profile docker

Results

• loglik.txt: file with the loglik estimates for each parameter setting.
• profiles.gz: compressed file with the probability of deletion of each segment.
• trajectories.gz: compressed file with the recombination events for sampled genome.
• run.info.txt: log of the workflow parameters.
• sampling-info.txt: informations about run performance (e.g. time, number of accepted samples).
• trajectories-stats.txt: statistics about each genome sampled by SPI.

Authors

• Giovanni Stracquadanio (giovanni.stracquadanio@ed.ac.uk)