diff --git a/biopet.wdl b/biopet.wdl index 8ac1d975faff8c5f1af8a58536e7a10c8b0b4489..554c75418aab199ad95035e8699ea59566184420 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -65,7 +65,7 @@ task SampleConfig { set -e -o pipefail ${preCommand} mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"} - java -Xmx${default=3 memory}G -jar ${tool_jar} \ + java -Xmx${default=3.0 memory}G -jar ${tool_jar} \ -i ${sep="-i " inputFiles} \ ${"--sample " + sample} \ ${"--library " + library} \ @@ -101,7 +101,7 @@ task BaseCounter { set -e -o pipefail ${preCommand} mkdir -p ${outputDir} - java -Xmx${default=12 memory}G -jar ${tool_jar} \ + java -Xmx${default=12.0 memory}G -jar ${tool_jar} \ -b ${bam} \ -r ${refFlat} \ -o ${outputDir} \ diff --git a/fastqc.wdl b/fastqc.wdl index cdda2f0168b2cfbf8daf4333b4aa060108b9a7e5..12b481ebb4ed2818dbadb9d62f6cc40538042841 100644 --- a/fastqc.wdl +++ b/fastqc.wdl @@ -69,7 +69,7 @@ task extractAdapters { command { set -e mkdir -p ${outputDir} - java -Xmx${default=4 memory}G -jar ${extractAdaptersFastqcJar} \ + java -Xmx${default=4.0 memory}G -jar ${extractAdaptersFastqcJar} \ --inputFile ${inputFile} \ ${"--adapterOutputFile " + adapterOutputFilePath } \ ${"--contamsOutputFile " + contamsOutputFilePath } \