Merge pull request #6396 from wm75/lofreq-log-fix

Make wildcards work as intended for collecting lofreq log files
galaxyproject · Oct 2, 2024 · 814935d · 814935d
2 parents f28d66c + 3734c4c
commit 814935d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tools/lofreq/lofreq_call.xml b/tools/lofreq/lofreq_call.xml
@@ -1,4 +1,4 @@
-<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01">
+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy3" profile="18.01">
     <description>with LoFreq</description>
     <macros>
         <import>macros.xml</import>
@@ -91,7 +91,7 @@
 
         ## in case of errors add the log files produced
         ## by the parallel workers to stderr
-        || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code)
+        || (tool_exit_code=\$? && cat "\$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code)
 
         ## work around a bug in lofreq call-parallel
         ## https://github.com/CSB5/lofreq/issues/85