From ef54c54f5dcf7fc093b0f9aa27ffdba6c069fd88 Mon Sep 17 00:00:00 2001
From: Tom Whalley <whalleyt@cardiff.ac.uk>
Date: Thu, 7 Nov 2024 14:41:23 +0000
Subject: [PATCH] update config for test

---
 testing.config | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/testing.config b/testing.config
index 9400bb5..e729f3f 100644
--- a/testing.config
+++ b/testing.config
@@ -51,7 +51,7 @@ params {
   output_dir = "${baseDir}/tests"
 
   // unmix myco 'yes' or 'no'
-  unmix_myco = 'yes'
+  unmix_myco = true
 
   // principal species in each sample, assuming genus Mycobacterium, default null
   // otherwise takes 1 of 10 values: abscessus, africanum, avium, bovis, chelonae, chimaera, fortuitum, intracellulare, kansasii, tuberculosis
@@ -66,28 +66,19 @@ params {
   // name of the bowtie index, e.g. hg19_1kgmaj
   bowtie_index_name = "hg19_1kgmaj"
 
-  // run VCFMIX 'yes' or 'no' (set to no for synthetic samples)
-  vcfmix = 'yes'
-
-  // path to AMR catalogue for gnomon
-  // https://github.com/oxfordmmm/tuberculosis_amr_catalogues available at path /tuberculosis_amr_catalogues in container
-  amr_cat = "/tuberculosis_amr_catalogues/catalogues/NC_000962.3/NC_000962.3_CRyPTIC_v1.311_GARC1_RUS.csv"
-
   // path to singularity recipes (needed for getversion)
   sing_dir = "${baseDir}/singularity"
 
-  // 'yes' to include mykrobe on final report, 'no' to include afanc in final report
-  mykrobe = 'yes'
 
   // path to the Afanc Myco database
   afanc_myco_db = "${baseDir}/Mycobacteriaciae_DB_3.0/"
   
   //resistance profiling
   resistance_profiler = "tb-profiler"
-  collate = "no"
+  collate = false
 
   //decontamination
-  permissive = "no"
+  permissive = false
 
 
 }