From 7e1bf51f20891e1b8e7e8a141081558231b569ae Mon Sep 17 00:00:00 2001
From: "Lataretu, Marie" <LataretuM@rki.de>
Date: Wed, 13 Sep 2023 17:27:44 +0200
Subject: [PATCH] fixed disabling of artic normalisation

If the disabling was activated in the pipeline (`--artic_normalize False`), no parameter was handed over to the artic pipeline, so that artic used the default value of 200.
Normalisation is now correctly turned off by passing `--normalise 0` to the artic pipeline.
---
 workflows/process/artic.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/process/artic.nf b/workflows/process/artic.nf
index 42f6896..cba69a5 100755
--- a/workflows/process/artic.nf
+++ b/workflows/process/artic.nf
@@ -23,7 +23,7 @@ process artic_medaka {
         tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
 
     script:   
-        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : ''
+        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0'
         """
         artic minion    --medaka \
                         --medaka-model ${params.medaka_model} \
@@ -89,7 +89,7 @@ process artic_medaka_custom_bed {
         tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
         tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
     script:   
-        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : ''
+        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0'
         """
         # create a new primer dir as input for artic
         mkdir -p primer_scheme/nCoV-2019
@@ -167,7 +167,7 @@ process artic_nanopolish {
         tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
         tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
     script:   
-        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : ''
+        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0'
         """
         artic minion --minimap2 \
             ${normalise_arg} \
@@ -234,7 +234,7 @@ process artic_nanopolish_custom_bed {
         tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
         tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
     script:   
-        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : ''
+        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : '--normalise 0'
         """
         # create a new primer dir as input for artic
         mkdir -p primer_scheme/nCoV-2019