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Commit d619ed18 authored by Ruben Vorderman's avatar Ruben Vorderman
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add extra operater to concatenateTextFiles

parent a5d69668
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2 merge requests!9Changes for virus assembly pipeline,!10Extra tasks required for assembly.
...@@ -51,12 +51,13 @@ task concatenateTextFiles { ...@@ -51,12 +51,13 @@ task concatenateTextFiles {
Array[File] fileList Array[File] fileList
String combinedFilePath String combinedFilePath
Boolean? unzip=false Boolean? unzip=false
Boolean? zip=false
command { command {
set -e -o pipefail set -e -o pipefail
${"mkdir -p $(dirname " + combinedFilePath + ")"} ${"mkdir -p $(dirname " + combinedFilePath + ")"}
${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \ ${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
> ${combinedFilePath} ${true="| gzip -c" false="" zip} > ${combinedFilePath}
} }
output { output {
......
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