Merge pull request #70 from rki-mf1/mason_read_quality_parameters

added mason_additional_args parameter

modules/mason/simulator/main.nf

@@ -39,7 +39,8 @@ process MASON_SIMULATOR {
         --fragment-max-size ${params.fragment_max_size} \
         --fragment-mean-size ${params.fragment_mean_size} \
         --fragment-size-std-dev ${params.fragment_size_std_dev} \
-        --illumina-read-length ${params.illumina_read_length}
+        --illumina-read-length ${params.illumina_read_length} \
+        ${params.mason_additional_args}
     """
 
 

nextflow.config

@@ -25,6 +25,7 @@ params {
     fragment_mean_size      = 500
     fragment_size_std_dev   = 20
     illumina_read_length    = 150
+    mason_additional_args   = ""
 
     // [LEGACY] Nanosim Oxford Nanopore (WGS) - Read simulation parameters
     dna_type        = 'linear'

src/Helppages.groovy

@@ -67,6 +67,7 @@ class Helper {
         ${c_green} --fragment_mean_size ${c_reset} mean size of fragments [default: ${params.fragment_mean_size}]
         ${c_green} --fragment_size_std_dev ${c_reset} standard deviation for fragment size [default: ${params.fragment_size_std_dev}]
         ${c_green} --illumina_read_length ${c_reset} read length of synthetic illumina reads [default: ${params.illumina_read_length}]
+        ${c_green} --mason_additional_args ${c_reset} additional arguments for mason_simulator [default: ${params.mason_additional_args}]
 
         ${c_yellow}Nanopore Sequencing parameter, optional if [--read_type ont] is supplied ${c_reset}