Merge pull request #319 from uclahs-cds/sfitz-fix-pon-check

fix check for panel of normals and add in log
uclahs-cds · Oct 28, 2024 · 51d781a · 51d781a
2 parents 0835f91 + b03b049
commit 51d781a
Show file tree

Hide file tree

Showing 5 changed files with 11 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add option to input VCFs for intersection
 - Add VAF stripplot for variant overlaps across tools
 
+### Fixed
+ - Avoid warning when run without panel of normals
+
 ## [8.1.0] - 2024-05-15
 
 ### Added

diff --git a/config/methods.config b/config/methods.config
@@ -93,6 +93,9 @@ methods {
             params.germline = false
         }
         params.germline_resource_gnomad_vcf_index = "${params.germline_resource_gnomad_vcf}.tbi"
+        if (!params.containsKey("panel_of_normals_vcf")) {
+            params.panel_of_normals_vcf = ""
+        }
     }
 
     check_valid_algorithms = {

diff --git a/module/mutect2-processes.nf b/module/mutect2-processes.nf
@@ -15,6 +15,7 @@ Mutect2 Options:
 - single tumor normal pair:       ${params.single_NT_paired}
 - germline resource:              ${params.germline_resource_gnomad_vcf}
 - contamination_table:            ${params.input.tumor.contamination_table}
+- panel of normals:               ${params.panel_of_normals_vcf}
 """
 
 process run_SplitIntervals_GATK {
@@ -92,7 +93,7 @@ process call_sSNV_Mutect2 {
     normal_names = normal_name.collect { "-normal ${it}" }.join(' ')
     bam = normal_names == '-normal NO_ID' ? "$tumors" : "$tumors $normals $normal_names"
     germline = params.germline ? "--germline-resource $germline_resource_gnomad_vcf" : ""
-    panel_of_normals = params.panel_of_normals_vcf ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""
+    panel_of_normals_cmd = params.panel_of_normals_vcf ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""
     interval_id = interval.baseName.split('-')[0]
     """
     set -euo pipefail
@@ -105,7 +106,7 @@ process call_sSNV_Mutect2 {
         -O ${params.output_filename}_unfiltered-${interval.baseName}.vcf.gz \
         --tmp-dir \$PWD \
         $germline \
-        $panel_of_normals \
+        $panel_of_normals_cmd \
         ${params.mutect2_extra_args}
     """
     }

diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -118,6 +118,7 @@
       "normal_id": "0192847",
       "output_dir": "/tmp/outputs",
       "output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847",
+      "panel_of_normals_vcf": "",
       "patient_id": "TWGSAMIN000001",
       "pipeval_version": "4.0.0-rc.2",
       "proc_resource_params": {

diff --git a/test/configtest-F32.json b/test/configtest-F32.json
@@ -118,6 +118,7 @@
       "normal_id": "0192847",
       "output_dir": "/tmp/outputs",
       "output_dir_base": "/tmp/outputs/call-sSNV-VER.SI.ON/0192847",
+      "panel_of_normals_vcf": "",
       "patient_id": "TWGSAMIN000001",
       "pipeval_version": "4.0.0-rc.2",
       "proc_resource_params": {