--- a/gemini_dump.xml	Fri Dec 14 12:35:04 2018 -0500
+++ b/gemini_dump.xml	Mon Dec 17 12:21:48 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
     <description>Extract data from the Gemini DB</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -23,7 +23,11 @@
 
         <param name="report" type="select" label="The information to be reported" help="(-t)">
             <option value="--variants">All rows/columns from the variants table (--variants)</option>
-            <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
+            <!-- The genotypes option is broken in gemini v0.20.1.
+            Add this option back in once there is an upstream fix!
+            Remember then to replace all underscores with dashes on the following line. They are only there to not break this comment!
+            <option value="__genotypes">All rows/columns from the variants table with one line per sample/genotype (__genotypes)</option>
+            -->
             <option value="--samples">All rows/columns from the samples table (--samples)</option>
         </param>
         <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
@@ -34,12 +38,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
             <param name="header" value="True" />
-            <param name="report" value="--genotypes" />
+            <param name="report" value="--samples" />
             <output name="outfile">
                 <assert_contents>
-                    <has_line_matching expression="chrom&#009;start&#009;end&#009;.*sample&#009;.*genotype.*" />
+                    <has_line_matching expression="sample_id&#009;family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype" />
                 </assert_contents>
             </output>
         </test>

--- a/gemini_macros.xml	Fri Dec 14 12:35:04 2018 -0500
+++ b/gemini_macros.xml	Mon Dec 17 12:21:48 2018 -0500
@@ -1,15 +1,12 @@
 <macros>
     <!-- gemini version to be used -->
-    <token name="@VERSION@">0.18.1</token>
+    <token name="@VERSION@">0.20.1</token>
     <!-- minimal annotation files version required by this version of gemini -->
-    <token name="@DB_VERSION@">181</token>
+    <token name="@DB_VERSION@">200</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">gemini</requirement>
-            <requirement type="package" version="0.2.6">tabix</requirement>
-            <!-- for conda useage -->
-            <!--requirement type="package" version="1.3.1">htslib</requirement-->
             <yield />
         </requirements>
     </xml>

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--- a/test-data/gemini_versioned_databases.loc	Fri Dec 14 12:35:04 2018 -0500
+++ b/test-data/gemini_versioned_databases.loc	Mon Dec 17 12:21:48 2018 -0500
@@ -1,3 +1,3 @@
 ## GEMINI versioned databases
 #DownloadDate	dbkey	DBversion	Description	Path
-1999-01-01	hg19	181	GEMINI annotations (test snapshot)	${__HERE__}/test-cache
+1999-01-01	hg19	200	GEMINI annotations (test snapshot)	${__HERE__}/test-cache

--- a/test-data/test-cache/gemini-config.yaml	Fri Dec 14 12:35:04 2018 -0500
+++ b/test-data/test-cache/gemini-config.yaml	Mon Dec 17 12:21:48 2018 -0500
@@ -2,12 +2,14 @@
 versions:
   ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4
   ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2
-  ExAC.r0.3.sites.vep.tidy.vcf.gz: 3
+  ExAC.r0.3.sites.vep.tidy.vcf.gz: 4
   GRCh37-gms-mappability.vcf.gz: 2
-  clinvar_20160203.tidy.vcf.gz: 5
+  clinvar_20170130.tidy.vcf.gz: 5
   cosmic-v68-GRCh37.tidy.vcf.gz: 3
-  dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4
+  dbsnp.b147.20160601.tidy.vcf.gz: 1
   detailed_gene_table_v75: 2
   geno2mp.variants.tidy.vcf.gz: 1
+  gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2
   hg19.rmsk.bed.gz: 2
   summary_gene_table_v75: 2
+  whole_genome_SNVs.tsv.compressed.gz: 2

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