Merge pull request #2060 from Clinical-Genomics/release/12.0.2

fixes #2057

Author: jemten

643594-miptest_metrics_deliverables.yaml

@@ -3,6 +3,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [12.0.2]
+
+- Fixes the relatedness check in mip qccollect
+
 ## [12.0.1]
 
 - Adds loqudb and gnomad frequencies to vcf2cytosure filtering

CHANGELOG.md

@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{12.0.1};
+Readonly our $MIP_VERSION => q{12.0.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

lib/MIP/Constants.pm

@@ -453,15 +453,6 @@ sub analysis_gatk_variantrecalibration_wes {
             }
         );
 
-        # Used to find order of samples in qccollect downstream
-        set_recipe_outfile_in_sample_info(
-            {
-                path             => $outfile_path,
-                recipe_name      => q{pedigree_check},
-                sample_info_href => $sample_info_href,
-            }
-        );
-
         submit_recipe(
             {
                 base_command                      => $profile_base_command,
@@ -917,15 +908,6 @@ sub analysis_gatk_variantrecalibration_wgs {
             }
         );
 
-        # Used to find order of samples in qccollect downstream
-        set_recipe_outfile_in_sample_info(
-            {
-                path             => $outfile_path,
-                recipe_name      => q{pedigree_check},
-                sample_info_href => $sample_info_href,
-            }
-        );
-
         submit_recipe(
             {
                 base_command                      => $profile_base_command,

lib/MIP/Recipes/Analysis/Gatk_variantrecalibration.pm

@@ -483,6 +483,17 @@ sub analysis_plink {
                     sample_info_href => $sample_info_href,
                 }
             );
+            if ($outfile_tag eq q{relation_check}) {
+
+                ## Used to identify samples in mibs
+                set_recipe_outfile_in_sample_info(
+                    {
+                        path             => $uniq_outfile_path,
+                        recipe_name      => q{pedigree_check},
+                        sample_info_href => $sample_info_href,
+                    }
+                );
+            }
 
         }
 

lib/MIP/Recipes/Analysis/Plink.pm

@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v12.0.1
+    uri: docker.io/clinicalgenomics/mip:v12.0.2
   multiqc:
     executable:
       multiqc: