Merge pull request galaxyproject#6621 from richard-burhans/update-hal…

…fdeep fixing mapped-reads symlinks
nilchia · Dec 11, 2024 · 6a77207 · 6a77207
2 parents d2208e8 + cfa6bb8
commit 6a77207
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
@@ -30,9 +30,9 @@
         ## mapped reads
         ##
         #if $mapped_reads
-            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' &&
-            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' &&
-            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' &&
+            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.bam' &&
+            ln -s '${reads_base}${reads.ext}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
+            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}{reads.ext}.sort.bam.bai' &&
         #end if
         ##
         ## run bam_depth.sh

diff --git a/tools/halfdeep/macros.xml b/tools/halfdeep/macros.xml
@@ -5,7 +5,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.1.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">
         <citations>