diff --git a/conf/modules.config b/conf/modules.config
index 5f4df7ab4..d31377543 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -795,7 +795,9 @@ process{
         ext.prefix = { "${meta.id}_SNP" }
         ext.args = "-AS -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
         publishDir = [
-            enabled: false
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/"},
+            pattern: "*{pdf,R}"
         ]
     }
 
diff --git a/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf b/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
index 8b1e9fa2f..30b265238 100644
--- a/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
+++ b/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
@@ -45,6 +45,7 @@ process GATK4_VARIANTRECALIBRATOR {
         --tranches-file ${prefix}.tranches \\
         $reference_command \\
         --tmp-dir . \\
+        --rscript-file output.plots.R \\
         $labels_command \\
         $args