Add input validation parameter for baseq

genepi · Dec 28, 2024 · 27e9086 · 27e9086
1 parent 1a449a3
commit 27e9086
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/cloudgene.yaml b/cloudgene.yaml
@@ -126,17 +126,17 @@ workflow:
     - id: min_mean_coverage
       description: Minimal Mean Coverage 
       type: number
-      visible: true
+      visible: false
       value: 50  
 
     - id: baseQ
-      description: Minimal Base Quality
+      description: Minimal Base Quality (Variant Calling)
       type: number
       visible: true 
-      value: 20  
+      value: 20
 
     - id: mapQ
-      description: Minimal Map Quality
+      description: Minimal Map Quality (Variant Calling)
       type: number
       visible: true
       value: 20      

diff --git a/modules/local/input_validation.nf b/modules/local/input_validation.nf
@@ -38,6 +38,7 @@ process INPUT_VALIDATION {
         --output-contig contig.txt \
         --report validation_report.txt \
         --min-mean-depth ${params.min_mean_coverage} \
+        --min-mean-base-quality ${params.min_mean_base_quality} \
         --tool ${params.mode}
     exit_code_a=\$?
 

diff --git a/nextflow.config b/nextflow.config
@@ -26,6 +26,7 @@ params {
     subsampling            = "off"
     subsampling_coverage   = 2000
     min_mean_coverage      = 50
+    min_mean_base_quality  = 10
 
 
     service = [