From badc78ad0e1f1425963dc36feaafa74f449c26c3 Mon Sep 17 00:00:00 2001
From: "bart.charbon" <b.charbon@umcg.nl>
Date: Thu, 13 Jul 2023 15:04:57 +0200
Subject: [PATCH] Bump vcf-report to 5.5.2

---
 config/nxf_vcf.config                                         | 2 +-
 install.sh                                                    | 2 +-
 utils/apptainer/build.sh                                      | 2 +-
 .../def/{vcf-report-5.5.1.def => vcf-report-5.5.2.def}        | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)
 rename utils/apptainer/def/{vcf-report-5.5.1.def => vcf-report-5.5.2.def} (81%)

diff --git a/config/nxf_vcf.config b/config/nxf_vcf.config
index 7fd4f570f..08b425d93 100644
--- a/config/nxf_vcf.config
+++ b/config/nxf_vcf.config
@@ -11,7 +11,7 @@ env {
   CMD_FILTERVEP = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-109.3.sif filter_vep"
   CMD_BGZIP = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-109.3.sif bgzip"
   CMD_SAMTOOLS= "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/samtools-1.17-patch1.sif samtools"
-  CMD_VCFREPORT="apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-5.5.1.sif"
+  CMD_VCFREPORT="apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-5.5.2.sif"
   CMD_VCFDECISIONTREE = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-3.5.4.sif"
   CMD_VCFINHERITANCEMATCHER = "apptainer exec --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-2.1.6.sif"
 
diff --git a/install.sh b/install.sh
index 001fb9f8f..d05a1fc8a 100755
--- a/install.sh
+++ b/install.sh
@@ -222,7 +222,7 @@ download_images() {
   files+=("samtools-1.17-patch1.sif")
   files+=("vcf-decision-tree-3.5.4.sif")
   files+=("vcf-inheritance-matcher-2.1.6.sif")
-  files+=("vcf-report-5.5.1.sif")
+  files+=("vcf-report-5.5.2.sif")
   files+=("vep-109.3.sif")
   files+=("manta-1.6.0.sif")
   files+=("gado-1.0.1.sif")
diff --git a/utils/apptainer/build.sh b/utils/apptainer/build.sh
index 588bf8f5e..349241375 100644
--- a/utils/apptainer/build.sh
+++ b/utils/apptainer/build.sh
@@ -91,7 +91,7 @@ main() {
   images+=("samtools-1.17-patch1")
   images+=("vcf-decision-tree-3.5.4")
   images+=("vcf-inheritance-matcher-2.1.6")
-  images+=("vcf-report-5.5.1")
+  images+=("vcf-report-5.5.2")
   images+=("manta-1.6.0")
   
   for i in "${!images[@]}"; do
diff --git a/utils/apptainer/def/vcf-report-5.5.1.def b/utils/apptainer/def/vcf-report-5.5.2.def
similarity index 81%
rename from utils/apptainer/def/vcf-report-5.5.1.def
rename to utils/apptainer/def/vcf-report-5.5.2.def
index 3a0b4e1c0..454d0e2c7 100644
--- a/utils/apptainer/def/vcf-report-5.5.1.def
+++ b/utils/apptainer/def/vcf-report-5.5.2.def
@@ -8,7 +8,7 @@ From: sif/build/openjdk-17.sif
 %post
     version_major=5
     version_minor=5
-    version_patch=1
+    version_patch=2
 
     # install
     apk update
@@ -16,7 +16,7 @@ From: sif/build/openjdk-17.sif
 
     mkdir -p /opt/vcf-report/lib
     curl -Ls -o /opt/vcf-report/lib/vcf-report.jar "https://github.com/molgenis/vip-report/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-report.jar"
-    echo "791302158bf4b87faf6415011afb62efcd2225f42c635e7fd05bc8181fb3bead  /opt/vcf-report/lib/vcf-report.jar" | sha256sum -c
+    echo "f10e0e2826b01ca81301f9c890b6f366a5eb3f14f62d7b932d103fe9e090af0a  /opt/vcf-report/lib/vcf-report.jar" | sha256sum -c
 
     # cleanup
     apk del .build-dependencies