From 652fbb94c52783654a2bc2b99c29d64e7d6636fa Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 5 Oct 2024 17:03:58 +0200
Subject: [PATCH] vcf2maf: fix wrong test parameter

---
 tools/vcf2maf/.lint_skip  | 1 -
 tools/vcf2maf/vcf2maf.xml | 8 ++++----
 2 files changed, 4 insertions(+), 5 deletions(-)
 delete mode 100644 tools/vcf2maf/.lint_skip

diff --git a/tools/vcf2maf/.lint_skip b/tools/vcf2maf/.lint_skip
deleted file mode 100644
index dabcb8dc984..00000000000
--- a/tools/vcf2maf/.lint_skip
+++ /dev/null
@@ -1 +0,0 @@
-TestsParamInInputs
diff --git a/tools/vcf2maf/vcf2maf.xml b/tools/vcf2maf/vcf2maf.xml
index b20388aaa28..1d5d7b0ced3 100644
--- a/tools/vcf2maf/vcf2maf.xml
+++ b/tools/vcf2maf/vcf2maf.xml
@@ -139,7 +139,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="history" />
 			<param name="ref" dbkey="hg19" value="test1.fa" ftype="fasta" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<assert_command>
 				<has_text text="--ncbi-build 'GRCh37'"/>
 			</assert_command>
@@ -149,7 +149,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="cached" />
 			<param name="ref" value="hg19test" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<assert_command>
 				<has_text text="--ncbi-build 'GRCh37'"/>
 			</assert_command>
@@ -159,7 +159,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="cached" />
 			<param name="ref" value="hg19test" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<param name="include_header" value="False" />
 			<output name="output1" ftype="tabular" >
 				<assert_contents>
@@ -172,7 +172,7 @@
 			<param name="input1" dbkey="dm6" value="input_test2.vcf" ftype="vcf" />
 			<param name="ref_source" value="history" />
 			<param name="ref" dbkey="dm6" value="test2.fa" ftype="fasta" />
-			<param name="source" value="restricted" />
+			<param name="annotation_cache|source" value="restricted" />
 			<param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
 			<assert_command>
 				<has_text text="--ncbi-build 'BDGP6.32'"/>