Add MTB_L10 reference in the bundled GVCF

README.md

@@ -309,9 +309,9 @@ containing GVCF reference dataset for ~600 samples is provided for augmenting sm
 
 
 ```
-use_ref_exit_rif_gvcf = false
-ref_exit_rif_gvcf =  "/path/to/FILE.g.vcf.gz" 
-ref_exit_rif_gvcf_tbi =  "/path/to/FILE.g.vcf.gz.tbi"
+use_ref_gvcf = false
+ref_gvcf =  "/path/to/FILE.g.vcf.gz" 
+ref_gvcf_tbi =  "/path/to/FILE.g.vcf.gz.tbi"
 ```
 
 > :bulb: **Custom GVCF dataset**: <br>

conf/test.config

@@ -9,7 +9,7 @@ params {
     compute_minor_variants = true
     dataset_is_not_contaminated = true
 
-    use_ref_exit_rif_gvcf = false
+    use_ref_gvcf = false
 
     //The path to resistance database to use for resistance calling
     resistance_db = "NONE"

default_params.config

@@ -15,9 +15,9 @@ vcf_name = "joint"
 
 // NOTE: Got little genetic diveristy in your dataset? (.e.g clonal or <20 samples) - use the EXIT-RIF GVCF file to include additional samples.
 
-use_ref_exit_rif_gvcf = true
-ref_exit_rif_gvcf =  "${projectDir}/resources/ref_gvcfs/LineagesAndOutgroup.g.vcf.gz" 
-ref_exit_rif_gvcf_tbi =  "${projectDir}/resources/ref_gvcfs/LineagesAndOutgroup.g.vcf.gz.tbi"
+use_ref_gvcf = true
+ref_gvcf =  "${projectDir}/resources/ref_gvcfs/LineagesAndOutgroup.g.vcf.gz" 
+ref_gvcf_tbi =  "${projectDir}/resources/ref_gvcfs/LineagesAndOutgroup.g.vcf.gz.tbi"
 
 // ##### The follow sections generally do not require adjusting. #####
 
@@ -69,7 +69,7 @@ skip_minor_variants_gatk = true
 //=========================================
 
 // Use this flag to disable downstream phylogenetic of merged GVCF
-skip_phylogeny_and_clustering = true //OR false
+skip_phylogeny_and_clustering = false //OR false
 
 // Use this flag to enable downstream analysis of merged GVCF
 skip_complex_regions = true //OR true

modules/gatk/combine_gvcfs.nf

@@ -18,7 +18,7 @@ process GATK_COMBINE_GVCFS {
 
     script:
 
-        def optionalRefExitRifGvcf  = ( params.use_ref_exit_rif_gvcf ) ? " --variant ${ref_exit_rif_gvcf} " : ""
+        def optionalRefExitRifGvcf  = ( params.use_ref_gvcf ) ? " --variant ${ref_exit_rif_gvcf} " : ""
 
         """
         ${params.gatk_path} CombineGVCFs --java-options "-Xmx${task.memory.giga}G" \\

workflows/subworkflows/prepare_cohort_vcf.nf

@@ -20,13 +20,13 @@ workflow PREPARE_COHORT_VCF {
             .dump(tag: "PREPARE_COHORT_VCF gvcfs_string_ch:", pretty: true)
 
 
-        if (params.use_ref_exit_rif_gvcf) {
+        if (params.use_ref_gvcf) {
             refExitRifGvcf = file(params.ref_exit_rif_gvcf, checkIfExists: true)
         } else {
             refExitRifGvcf = []
         }
 
-        if (params.use_ref_exit_rif_gvcf) {
+        if (params.use_ref_gvcf) {
             refExitRifGvcfTbi = file(params.ref_exit_rif_gvcf_tbi, checkIfExists: true)
         } else {
             refExitRifGvcfTbi = []