update readme

resources/auxiliary_workflows/benchmark/README.md

@@ -1,6 +1,6 @@
-# Quasispecies Reconstruction Benchmark
+# Benchmarking module
 
-Benchmark Quasispecies assembly methods both on the level of local as well as global haplotypes.
+Benchmark Quasispecies assembly methods both on the level of SNVs as well as global haplotypes.
 
 ## Usage
 
@@ -23,3 +23,25 @@ Conda packages can be added by writing `# CONDA: <package name> = <version>`.
 Analogously, PIP packages can be added by writing `# PIP: <package name>`.
 Multiple packages can be added by repeating these lines.
 A conda environment will then be dynamically generated (when running Snakemake with `--use-conda`).
+
+
+## Configuring your benchmarking study
+
+### Configuration file
+`method_list` List of methods that should be executed. Methods should be defined as described above.  
+`replicate_count` Number of replicates per line in `params.csv` that should be created.
+`haplotype_generation` Either `distance` or `mutation_rate`. In `distance` haplotypes are generated based on distance pattern, in the mode `mutation_rate` haplotypes are based on mutation, deletion and insertion rates indicated in the column `haplos` in `params.csv`.
+`params_path` File path to parameter file `params.csv`.
+`master_seq_path` Path to fasts file of master sequence that should be used for the generation of the haplotype population.
+
+### Parameter file
+This is a `csv`-file with the following columns:
+`seq_tech` illumina, nanopore or pacbio
+`seq_mode` shotgun, only for `illumina` we also have amplicon, in case of single_amplicon
+`seq_mode_param` Parameters for amplicon mode. read_lenght:overlap.
+`read_length` Read length
+`genome_size` Genome size
+`coverage` Coverage  
+`haplos`for distance mode: haplos = n_group1,n_group2,d_group12,d_group1,d_group2,freq_dist,freq_param
+for mutation mode: haplos = mutation_rate,insertion_rate,deletion_rate,haplotype_pattern
+parameters are seperated with "@"