From bdff37c3d7c880f599af223504808306e75e2d76 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 15:33:27 +0200
Subject: [PATCH] Added the statistical tests and conversion to vcf

---
 modules/vardictjava/main.nf               | 7 ++++++-
 tests/modules/vardictjava/nextflow.config | 1 +
 tests/modules/vardictjava/test.yml        | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index a28cb539..92051074 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -21,17 +21,22 @@ process VARDICTJAVA {
 
     script:
     def args = task.ext.args ?: ''
+    def args_conversion = task.ext.args_conversion ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     vardict-java \\
         $args \\
-        -c 1 -S 2 -E 3 -h \\
+        -c 1 -S 2 -E 3 \\
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
+        | teststrandbias.R \\
+        | var2vcf_valid.pl \\
+            $args_conversion \\
+            -N $prefix \\
         | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config
index 5dc176a9..fc698f59 100644
--- a/tests/modules/vardictjava/nextflow.config
+++ b/tests/modules/vardictjava/nextflow.config
@@ -4,5 +4,6 @@ process {
     
     withName: VARDICTJAVA {
         ext.args = ''
+        ext.args_conversion = ''
     }
 }
\ No newline at end of file
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 77aa9047..549d688e 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 2179dcaee6183495b421293f42db11b5
+      md5sum: 3f1f227afc532bddeb58f16fd3013fc8
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96