some debugging

bioconda.wdl

@@ -20,5 +20,6 @@ task installPrefix {
     }
     output {
         File condaEnvPath=prefix
+        File condaJson=stdout()
     }
  }

cutadapt.wdl

@@ -97,7 +97,7 @@ task cutadapt {
         ${read1} ${read2}
     }
     output{
-        File report = file(stdout())
+        File report = stdout()
         File cutRead1 = read1output
         File? cutRead2 = read2output
         File? tooLongOutput=tooLongOutputPath

fastqc.wdl

@@ -39,7 +39,7 @@ task fastqc {
     }
 
     output {
-        String reportDir = outdirPath + "/" + sub(basename(seqFile),"\..*$","_fastqc")
+        String reportDir = outdirPath + "/" + sub(basename(seqFile), "..*$", "_fastqc")
         File rawReport = reportDir + "/fastqc_data.txt"
         File htmlReport = reportDir + "fastqc_report.html"
         File summary = reportDir + "/summary.txt"