Commit 7251bf27 authored by Boom's avatar Boom
Browse files

Fix lima output naming.

parent a095517d
......@@ -91,13 +91,13 @@ task Lima {
dirName="$(dirname ~{outputPrefix})"
find "$(cd ${dirName}; pwd)" -name "*.bam" > bamFiles.txt
find "$(cd ${dirName}; pwd)" -name "*.bam.pbi" > bamIndexes.txt
find "$(cd ${dirName}; pwd)" -name "*.subreadset.xml" > subreadsets.txt
find "$(cd ${dirName}; pwd)" -name "*.consensusreadset.xml" > consensusreadset.txt
>>>
output {
Array[File] limaBam = read_lines("bamFiles.txt")
Array[File] limaBamIndex = read_lines("bamIndexes.txt")
Array[File] limaXml = read_lines("subreadsets.txt")
Array[File] limaXml = read_lines("consensusreadset.txt")
File limaStderr = outputPrefix + ".lima.stderr.log"
File limaJson = outputPrefix + ".json"
File limaCounts = outputPrefix + ".lima.counts"
......
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