fix

README.md

@@ -27,7 +27,7 @@ If you encounter any problems, feel free to open an issue [here](https://github.
 
 ## Version History
 
-[Version 2.0.3 - Version 2.0.6](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.7) - Fix QC issues and remove HTSJDK index creation for input validation and QC.
+[Version 2.0.3 - Version 2.0.6](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.8) - Fix QC issues and remove HTSJDK index creation for input validation and QC.
 
 [Version 2.0.2](https://github.com/bystrogenomics/imputationserver2/releases/tag/v2.0.2) - Set minimac4 tmp directory (required for larger sample sizes).
 

modules/local/input_validation/input_validation_vcf.nf

@@ -10,7 +10,7 @@ process INPUT_VALIDATION_VCF {
 
     output:
     path("validated_vcfs/*.vcf.gz"), emit: validated_files
-    path("skipped_vcfs/*.vcf.gz"), emit: skipped_files
+    path("skipped_vcfs/*.vcf.gz"), emit: skipped_files, optional: true
     path("validation_report.txt"), emit: validation_report
 
     script:
@@ -161,17 +161,23 @@ EOF
             vcf_files_to_validate+=("\$f")
             mv "\$f" validated_vcfs/
 
-            if [ -f "\$f.csi" ] || [ -f "\$f.tbi" ]; then
-                mv "\$f".csi validated_vcfs/
-                mv "\$f".tbi validated_vcfs/
+            if [ -f "\$f.csi" ] ; then
+                mv "\$f.csi" validated_vcfs/
+            fi
+
+            if [ -f "\$f.tbi" ]; then
+                mv "\$f.tbi" validated_vcfs/
             fi
         else
             skipped_vcfs+=("\$f")
             mv "\$f" skipped_vcfs/
 
-            if [ -f "\$f.csi" ] || [ -f "\$f.tbi" ]; then
-                mv "\$f".csi skipped_vcfs/
-                mv "\$f".tbi skipped_vcfs/
+            if [ -f "\$f.csi" ] ; then
+                mv "\$f.csi" skipped_vcfs/
+            fi
+
+            if [ -f "\$f.tbi" ]; then
+                mv "\$f.tbi" skipped_vcfs/
             fi
         fi
     done

nextflow.config

@@ -1,6 +1,6 @@
 manifest {
     name            = 'imputationserver2'
-    version         = 'v2.0.7'
+    version         = 'v2.0.8'
     description     = 'Genotype Imputation Server 2'
     author          = 'Lukas Forer & Sebastian Schönherr'
     homePage        = 'https://github.com/bystrogenomics/imputationserver2'
@@ -98,7 +98,7 @@ profiles {
 
     docker.enabled            = true
     singularity.enabled       = false
-    process.container         = 'bystrogenomics/imputationserver2:v2.0.7'
+    process.container         = 'bystrogenomics/imputationserver2:v2.0.8'
 
     test {
         includeConfig 'conf/test.config'