Mercurial > repos > iuc > halfdeep

diff halfdeep.xml @ 2:ab8373ba3830 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep commit 8c89adcf33dc75d6bd315369bdeadb26fb6c17f9
author iuc
date Thu, 12 Dec 2024 22:09:19 +0000
parents a53e299fe1cb
children
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--- a/halfdeep.xml	Thu Dec 12 09:08:40 2024 +0000
+++ b/halfdeep.xml	Thu Dec 12 22:09:19 2024 +0000
@@ -30,9 +30,9 @@
         ## mapped reads
         ##
         #if $mapped_reads
-            ln -s '$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' &&
+            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