Set 2000x subsampling to default

genepi · Mar 7, 2024 · f2d760c · f2d760c
1 parent b82d38b
commit f2d760c
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/cloudgene.yaml b/cloudgene.yaml
@@ -101,18 +101,20 @@ workflow:
         0.1: 0.1      
 
     - id: coverage_estimation
-      description: Apply Coverage Estimate
+      description: Apply VAF Coverage Estimation
       type: list
       value: off
       values:
         on: On
         off: Off
 
     - id: subsampling
-      description: Coverage Subsampling (0 means deactivated)
+      description: Subsample to 2000x
       type: number
       visible: true 
-      value: 0  
+      values:
+        on: On
+        off: Off 
 
     - id: myseparator0
       type: separator

diff --git a/nextflow.config b/nextflow.config
@@ -23,7 +23,8 @@ params {
     alignQ                 = 30
     coverage_estimation    = "on"
     max_samples            = 0
-    subsampling            = 0
+    subsampling            = "on"
+    subsampling_coverage   = 2000
 
 
     service = [

diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf
@@ -84,10 +84,10 @@ workflow MTDNA_SERVER_2 {
 
     validated_files = INPUT_VALIDATION.out.validated_files.flatten()
 
-    if(params.subsampling != 0) {
+    if(params.subsampling.equals("on") ) {
         SUBSAMPLING (
             validated_files,
-            params.subsampling
+            params.subsampling_coverage
         )
         validated_files = SUBSAMPLING.out.subsampled_bam_ch
     }