Added variantrecalibrator plot and publish

wtsi-hgi · Oct 26, 2023 · af33661 · af33661
1 parent bc720e4
commit af33661
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git 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