getConfiguration task

fastqc.wdl

@@ -94,4 +94,20 @@ task extractAdapters {
         Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
         Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
     }
+}
+
+task getConfiguration {
+    String? preCommand
+    String? fastqcDirFile = "fastqcDir.txt"
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        echo $(dirname $(readlink -f $(which fastqc))) > ${fastqcDirFile}
+    }
+    output {
+        String fastqcDir = read_string(fastqcDirFile)
+        File adapterList = fastqcDir + "/Configuration/adapter_list.txt"
+        File contaminantList = fastqcDir + "/Configuration/contaminant_list.txt"
+        File limits = fastqcDir + "/Configuration/limits.txt"
+    }
 }
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