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LaraFuhrmann committed Apr 19, 2024
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Expand Up @@ -5,8 +5,8 @@ The notebooks in the directory `workflow/notebooks/` can be used to reproduce th
Here is a step-by-step guide on how to run this workflow.
1. Clone the repository of V-pipe 3.0 into your working directory: `git clone https://github.com/cbg-ethz/V-pipe.git`
2. Go into the directory of the benchmarking study for the global haplotype reconstruction `cd V-pipe/resources/auxiliary_workflows/benchmark/resources/multi_setup`
3. The parameters to reproduce the synthetic dataset of varying coverage is here: `config_distance_varycoverage/params.csv` with the configuration file `config_distance_varycoverage/config.yaml` where simulation mode, replicate number and methods to be executed are defined.
4. The parameters to reproduce the synthetic dataset of varying distance pattern is here: `config_distance_varyparams/params.csv` with the configuration file `config_distance_varyparams/config.yaml` where simulation mode, replicate number and methods to be executed are defined.
3. The parameters to reproduce the synthetic dataset of varying coverage is here: `config_varycoverage/params.csv` with the configuration file `config_varycoverage/config.yaml` where simulation mode, replicate number and methods to be executed are defined.
4. The parameters to reproduce the synthetic dataset of varying distance pattern is here: `config_varyparams/params.csv` with the configuration file `config_varyparams/config.yaml` where simulation mode, replicate number and methods to be executed are defined.
5. The parameters to reproduce the real dataset is here: `config_realdata/params.csv` with the configuration file `config_realdata/config.yaml` where replicate number and methods to be executed are defined.
6. The methods to execute must be define in a Python script in this directory: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions`
- Haploclique: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploclique.py`
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