update config for test

Author: t-whalley

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
 
 
 }