Fixed if

5ba7837c · Peter van 't Hof · ba792ad0 · 5ba7837c
Commit 5ba7837c authored 7 years ago by Peter van 't Hof
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -8,7 +8,8 @@ task FastqSplitter {
    command {
    mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
    if [ ${numberChunks} -gt 1 ]; then
-        java -jar ${tool_jar} -I ${inputFastq} -o ${sep='/${basename(inputFastq)} -o ' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
+        SEP="/${basename(inputFastq)} -o "
+        java -jar ${tool_jar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
    else
        ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
    fi