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Commit 0bf8c70f authored by Ruben Vorderman's avatar Ruben Vorderman
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change camelization

parent 9b7c5ff9
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1 merge request!47Fix fastqc and cutadapt for use with WDL 1.0
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...@@ -61,12 +61,12 @@ task Cutadapt { ...@@ -61,12 +61,12 @@ task Cutadapt {
String? reportPath String? reportPath
} }
String read2outputarg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else "" String read2outputArg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else ""
command { command {
set -e -o pipefail set -e -o pipefail
~{"mkdir -p $(dirname " + read1output + ")"} ~{"mkdir -p $(dirname " + read1output + ")"}
~{read2outputarg} ~{read2outputArg}
~{"mkdir -p $(dirname " + reportPath + ")"} ~{"mkdir -p $(dirname " + reportPath + ")"}
~{preCommand} ~{preCommand}
cutadapt \ cutadapt \
......
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