--- a/rg_rnaStar.xml	Fri Jul 02 20:18:29 2021 +0000
+++ b/rg_rnaStar.xml	Wed Sep 08 14:35:09 2021 +0000
@@ -52,11 +52,15 @@
         #end for
         #if str($twopass.twopassMode) != 'None':
             #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
-                #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
-                    ## case of cached index without built-in gene model,
-                    ## when user does not supply the optional gtf, but
-                    ## specifies the splice junction overhang
-                    --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
+                ## need to check first if its a cached index or from history
+                ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided
+                #if str($refGenomeSource.geneSource) == 'history':
+                    #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
+                       ## case of cached index without built-in gene model,
+                       ## when user does not supply the optional gtf, but
+                       ## specifies the splice junction overhang
+                       --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
+                    #end if
                 #end if
             #end if
         #end if
@@ -834,6 +838,42 @@
             <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
         </test>
+        <!-- test Basic twopass with a built-in gtf index option -->
+        <test expect_num_outputs="3">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="single" />
+                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+            </conditional>
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="indexed" />
+                <conditional name="GTFconditional">
+                    <param name="GTFselect" value="with-gtf" />
+                    <param name="genomeDir" value="001" />
+                </conditional>
+            </conditional>
+            <conditional name="twopass">
+                <param name="twopassMode" value="Basic" />
+            </conditional>
+            <section name="oformat">
+                <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
+                <param name="outSAMmapqUnique" value="255" />
+            </section>
+            <section name="filter">
+                <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
+                <conditional name="output_params2">
+                    <param name="output_select2" value="yes" />
+                </conditional>
+            </section>
+            <section name="algo">
+                <conditional name="params">
+                    <param name="settingsType" value="full" />
+                </conditional>
+            </section>
+
+            <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
+            <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
+        </test>
         <!-- test "multisample" twopass -->
         <test expect_num_outputs="3">
             <conditional name="singlePaired">