Keeping the linter happy: README.md titles

resources/auxiliary_workflows/benchmark/resources/multi_setup/README.md

@@ -1,3 +1,5 @@
+# Benchmarking
+
 This repository contains the Snakemake workflow to reproduce the benchmarking study for the global haplotype reconstruction methods presented in https://doi.org/10.1101/2023.10.16.562462.
 
 The notebooks in the directory `workflow/notebooks/` can be used to reproduce the figures of Figure 4.
@@ -9,10 +11,10 @@ Here is a step-by-step guide on how to run this workflow.
 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`  
-- PredictHaplo: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo.py`  
-- HaploConduct: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploconduct.py`  
-- CliqueSNV: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/cliquesnv.py`
+   - Haploclique: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploclique.py`  
+   - PredictHaplo: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo.py`  
+   - HaploConduct: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploconduct.py`  
+   - CliqueSNV: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/cliquesnv.py`
 7. Now the workflow is ready, go back to the directory `V-pipe/resources/auxiliary_workflows/benchmark/resources/multi_setup`.   
 8. To install the needed Conda environments execute: `snakemake --conda-create-envs-only --use-conda -c1`.   
 9. To submit the workflow to a lsf-cluster execute `./run_workflow.sh`, otherwise execute the workflow with `snakemake --use-conda -c1`