diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala index 8c0e3de2d85f2651fa7d0e1a0e0ff036708bac0b..de8b4efdc6c0494344945340d50096eb0609a990 100644 --- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala +++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Zcat.scala @@ -6,13 +6,13 @@ import org.broadinstitute.sting.commandline._ import java.io.File class Zcat(val globalConfig: Config) extends CommandLineFunction { - def this() = this(new Config(Map())) - this.analysisName = "zcat" - val config: Config = globalConfig.getAsConfig("zcat") - logger.debug("Config for " + this.analysisName + ": " + config) - - @Input(doc="Zipped file") var in: File = _ - @Output(doc="Unzipped file") var out: File = _ - - def commandLine = "zcat %s > %s".format(in, out) + def this() = this(new Config(Map())) + this.analysisName = "zcat" + val config: Config = globalConfig.getAsConfig("zcat") + logger.debug("Config for " + this.analysisName + ": " + config) + + @Input(doc="Zipped file") var in: File = _ + @Output(doc="Unzipped file") var out: File = _ + + def commandLine = "zcat %s > %s".format(in, out) } \ No newline at end of file diff --git a/flexiprep/examples/test.json b/flexiprep/examples/test.json index 59469ffd404c0c566e0a6c5ea8b776859422c5b1..9a50037eec4e1fbfec7be768edd9d3400816be57 100644 --- a/flexiprep/examples/test.json +++ b/flexiprep/examples/test.json @@ -2,6 +2,7 @@ "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" }, "flexiprep": { + "native_link": true, "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}