From 7470754faaa502877cbf4bad74ee0446c3cc7c13 Mon Sep 17 00:00:00 2001
From: TernovojD <ternovojd@hpc-login02.rki.local>
Date: Fri, 23 Aug 2024 15:19:19 +0200
Subject: [PATCH 1/2] added mason_additional_args parameter

---
 modules/mason/simulator/main.nf | 3 ++-
 nextflow.config                 | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/mason/simulator/main.nf b/modules/mason/simulator/main.nf
index 8a272eb..7ca1076 100644
--- a/modules/mason/simulator/main.nf
+++ b/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}
     """
 
 
diff --git a/nextflow.config b/nextflow.config
index e3169ec..ea8d256 100644
--- a/nextflow.config
+++ b/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'

From efa1a797fe35e6f6ee43ebb01c1a43f552d5cd95 Mon Sep 17 00:00:00 2001
From: TernovojD <ternovojd@hpc-login02.rki.local>
Date: Fri, 23 Aug 2024 16:31:26 +0200
Subject: [PATCH 2/2] added mason_additional_args parameter to help page

---
 src/Helppages.groovy | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Helppages.groovy b/src/Helppages.groovy
index 3420440..772fbd0 100644
--- a/src/Helppages.groovy
+++ b/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}