Merge pull request #13991 from mvdbeek/backport_compression_converter

[22.01] Don't create a BGZF index when running the compressing converter
galaxyproject · Jun 2, 2022 · 55a8ab1 · 55a8ab1
2 parents 468d5e0 + 4588b8f
commit 55a8ab1
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/lib/galaxy/datatypes/converters/uncompressed_to_gz.xml b/lib/galaxy/datatypes/converters/uncompressed_to_gz.xml
@@ -1,19 +1,19 @@
 <tool id="CONVERTER_uncompressed_to_gz" name="Convert uncompressed file to compressed" hidden="true" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <macros>
-        <token name="@TOOL_VERSION@">1.11</token>
+        <token name="@TOOL_VERSION@">1.15.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
-        <requirement type="package" version="1.11">tabix</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">htslib</requirement>
     </requirements>
     <command><![CDATA[
-cp '$ext_config' 'galaxy.json' &&
-bgzip -@ \${GALAXY_SLOTS:-1} -ci '$input1' > '$output1'
+cp '$ext_config' galaxy.json &&
+bgzip -@ "\${GALAXY_SLOTS:-1}" -c '$input1' > '$output1'
     ]]></command>
     <configfiles>
         <configfile name="ext_config">{"output1": {
-  "name": "${input1.name+'.gz' if not $input1.name.endswith('.vcf') else $input1.name+'.bgzip'} compressed",
-  "ext": "${input1.ext+'.gz' if $input1.ext != 'vcf' else 'vcf_bgzip'}"
+  "name": "${input1.name + '.gz' if not $input1.name.endswith('.vcf') else $input1.name + '.bgzip'} compressed",
+  "ext": "${input1.ext + '.gz' if $input1.ext != 'vcf' else 'vcf_bgzip'}"
 }}</configfile>
     </configfiles>
     <inputs>