update readme

resources/auxiliary_workflows/benchmark/README.md

@@ -28,20 +28,20 @@ A conda environment will then be dynamically generated (when running Snakemake w
 ## 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.
+`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 "@"
+This is a `csv`-file with the following columns:  
+`seq_tech` The following sequencing technologies can be simulated: `illumina`, `nanopore` or `pacbio`.  
+`seq_mode` Two modes are possible: `shotgun` is distributing reads randomly along the genome; `amplicon` mode is generating an amplicon scheme based on the parameters given in `seq_mode_param`. Note that the `amplicon` mode is only available with `illumina` as `seq_tech`.  
+`seq_mode_param` Parameters for`amplicon` mode. Read length and overlap of reads for the simulation of the amplicon scheme (`read_lenght:overlap` seperated by `:`). It is also possible to set it to `single_amplicon`, in this setting an artifical bed file is generated with one single amplicon across the whole genome. Parameters for amplicon mode.  
+`read_length` Read length of generated reads.   
+`genome_size` Genome size of the master sequence.    
+`coverage` Mean coverage per position in sample.     
+`haplos` There are two modes for the haplotype population as specified in the configuration file. Parameters are seperated with "@":  
+- For distance mode: haplos = n_group1,n_group2,d_group12,d_group1,d_group2,freq_dist,freq_param   
+- or mutation mode: haplos = mutation_rate,insertion_rate,deletion_rate,haplotype_pattern