mention EXIT-RIF DOI and update the parameter

TORCH-Consortium · Jul 26, 2023 · eafcb77 · eafcb77
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Showing 3 changed files with 7 additions and 8 deletions.
diff --git a/README.md b/README.md
@@ -14,8 +14,10 @@ MAGMA (**M**aximum **A**ccessible **G**enome for **M**tb **A**nalysis) is a pipe
   - Execution (software) requirements (`conf/docker.config` or `conf/conda.config`)
 - An (optional) GVCF reference dataset for ~600 samples is provided for augmenting smaller datasets
 
-> **Note**
-Downloading the reference EXIT_RIF GVCF files from FIXME
+
+# (Optional) GVCF for analyzing small number of samples
+
+You can download the  `EXIT_RIF GVCF` files from https://zenodo.org/record/8054182
 
 ## Tutorials and Presentations
 

diff --git a/default_params.config b/default_params.config
@@ -53,13 +53,10 @@ ntm_fraction_cutoff = 0.20
 // Set this to true if you'd like to only validate input fastqs
 only_validate_fastqs = false // OR true
 
-// Set this to true if you'd like to only validate input fastqs
-skip_merge_analysis = false // OR true
-
 // ##### EXPERIENCED USERS ##### 
 
-//Use this flag to skip the final merge
-skip_merge = false
+//Use this flag to skip the final merge analysis
+skip_merge_analysis = false // OR true
 
 // MAGMA optimises VQSR, if this messes up use the default settings for VQSR
 optimize_variant_recalibration = true

diff --git a/main.nf b/main.nf
@@ -25,7 +25,7 @@ workflow {
 
         VALIDATE_FASTQS_WF(params.input_samplesheet)
 
-    } else if (params.only_pre_merge_analysis) {
+    } else if (params.skip_merge_analysis) {
 
         validated_reads_ch = VALIDATE_FASTQS_WF( params.input_samplesheet )