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Commit 7487eba2 authored by ffinfo's avatar ffinfo
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Fixing read_lines

parent cc899a63
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1 merge request!51Fixing outputs
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with 2 additions and 4 deletions
biopet.wdl
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− 4
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...@@ -97,8 +97,6 @@ task ExtractAdaptersFastqc { ...@@ -97,8 +97,6 @@ task ExtractAdaptersFastqc {
set -e set -e
~{preCommand} ~{preCommand}
mkdir -p ~{outputDir} mkdir -p ~{outputDir}
touch ~{adapterOutputFilePath}
touch ~{contamsOutputFilePath}
~{toolCommand} \ ~{toolCommand} \
--inputFile ~{inputFile} \ --inputFile ~{inputFile} \
~{"--adapterOutputFile " + adapterOutputFilePath } \ ~{"--adapterOutputFile " + adapterOutputFilePath } \
...@@ -113,8 +111,8 @@ task ExtractAdaptersFastqc { ...@@ -113,8 +111,8 @@ task ExtractAdaptersFastqc {
output { output {
File adapterOutputFile = adapterOutputFilePath File adapterOutputFile = adapterOutputFilePath
File contamsOutputFile = contamsOutputFilePath File contamsOutputFile = contamsOutputFilePath
Array[String] adapterList = read_lines(adapterOutputFilePath) Array[String] adapterList = read_lines(adapterOutputFile)
Array[String] contamsList = read_lines(contamsOutputFilePath) Array[String] contamsList = read_lines(contamsOutputFile)
} }
runtime { runtime {
......
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