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Commit 58300734 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added conda env

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...@@ -121,7 +121,6 @@ task FastqSync { ...@@ -121,7 +121,6 @@ task FastqSync {
task SampleConfig { task SampleConfig {
String? preCommand String? preCommand
String tool_jar
Array[File]+ inputFiles Array[File]+ inputFiles
String keyFilePath String keyFilePath
String? sample String? sample
...@@ -138,7 +137,7 @@ task SampleConfig { ...@@ -138,7 +137,7 @@ task SampleConfig {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"} mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
java -Xmx${mem}G -jar ${tool_jar} \ biopet-sampleconfig -Xmx${mem}G \
-i ${sep="-i " inputFiles} \ -i ${sep="-i " inputFiles} \
${"--sample " + sample} \ ${"--sample " + sample} \
${"--library " + library} \ ${"--library " + library} \
......
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