Issue 509 & 313

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#507](https://github.com/nf-core/sarek/pull/507) - Subway map for building indexes
 - [#512](https://github.com/nf-core/sarek/pull/512) - Subway map for pipeline
 - [#522](https://github.com/nf-core/sarek/pull/522) - Add QC for vcf files & MultiQC
+- [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--only_paired_variant_calling` to allow skipping of germline variantcalling for paired samples
 
 ### Changed
 

nextflow.config

@@ -51,6 +51,7 @@ params {
     sequencing_center = null // No sequencing center to be written in BAM header by aligner
 
     // Variant Calling
+    only_paired_variant_calling = false //if true, skips germline variant calling for normal-paired samples
     ploidy = 2          //null (in ascat, test this works) // Use default value, you can use 2,3,4
     ascat_purity = null // Use default value
     cf_coeff = 0.05                     // default value for Control-FREEC

nextflow_schema.json

@@ -232,6 +232,11 @@
             "default": "",
             "fa_icon": "fas fa-toolbox",
             "properties": {
+                "only_paired_variant_calling": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-angle-double-right",
+                    "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools."
+                },
                 "ploidy": {
                     "type": "number",
                     "fa_icon": "fas fa-bacon",

workflows/sarek.nf

@@ -627,6 +627,22 @@ workflow SAREK {
         // and remove patient ID field & null value for further processing [meta1, [cram1,crai1]] [meta2, [cram2,crai2]]
         cram_variant_calling_tumor_only = cram_variant_calling_tumor_filtered.transpose().map{ it -> [it[1], it[2], it[3]] }
 
+        if(params.only_paired_variant_calling){
+            // Normal only samples
+
+            // 1. Join with tumor samples, in each channel there is one key per patient now. Patients without matched tumor end up with: [patient1, [meta1], [cram1,crai1], null] as there is only one matched normal possible
+            cram_variant_calling_normal_joined = cram_variant_calling_normal_to_cross.join(cram_variant_calling_tumor_grouped, remainder: true)
+
+            // 2. Filter out entries with last entry null
+            cram_variant_calling_normal_filtered = cram_variant_calling_normal_joined.filter{ it ->  !(it.last()) }
+
+            // 3. Remove patient ID field & null value for further processing [meta1, [cram1,crai1]] [meta2, [cram2,crai2]] (no transposing needed since only one normal per patient ID)
+            cram_variant_calling_status_normal = cram_variant_calling_normal_filtered.map{ it -> [it[1], it[2], it[3]] }
+
+        }else{
+            cram_variant_calling_status_normal = cram_variant_calling_status.normal
+        }
+
         // Tumor - normal pairs
         // Use cross to combine normal with all tumor samples, i.e. multi tumor samples from recurrences
         cram_variant_calling_pair = cram_variant_calling_normal_to_cross.cross(cram_variant_calling_pair_to_cross)
@@ -641,9 +657,10 @@ workflow SAREK {
                 [meta, normal[2], normal[3], tumor[2], tumor[3]]
             }
 
+
         // GERMLINE VARIANT CALLING
         GERMLINE_VARIANT_CALLING(
-            cram_variant_calling_status.normal,
+            cram_variant_calling_status_normal,
             dbsnp,
             dbsnp_tbi,
             dict,