From a26835da3085eed8646a5ef2824593b6a4693a7c Mon Sep 17 00:00:00 2001
From: EladH1 <eladherz1@gmail.com>
Date: Wed, 22 Jan 2025 19:26:12 +0100
Subject: [PATCH] full_test.config updates

---
 conf/test_full.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/test_full.config b/conf/test_full.config
index 60a139c..d22b5ed 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -20,7 +20,7 @@ params {
     max_time            = '8.h'
 
     // Input data
-    input               = 'assets/samplesheet_full_small.csv'
+    input               = "${projectDir}/assets/samplesheet_full_small.csv"
     outdir              = 'results'
 
     // Genome references
@@ -28,7 +28,7 @@ params {
     analysis            = 'germline'
     variant_type        = "small"
     method              = 'happy,rtgtools'
-    preprocess          = "normalization,deduplication,filter_contigs"
+    preprocess          = "normalize,deduplicate,filter_contigs"
 
     truth_id            = "HG002"
     truth_vcf           = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/SupplementaryFiles/HG002_GRCh37_1_22_v4.2.1_highconf.vcf.gz"