Fix a typo and export a function only used in one module to that modu…

…le. Part of #107

main.nf

@@ -362,14 +362,6 @@ def get_read_type(f) {
   }
 }
 
-def get_file_ext(f) {
-  if (f.name.toString().tokenize(".")[-1] == "gz") {
-    return('.fastq.gz')
-  } else {
-    return('.fastq')
-  }
-}
-
 //  Given a "row" of the 'samples.manifest' file as a string, return the FASTQ
 //  files
 def get_fastq_names(row) {
@@ -464,7 +456,7 @@ include { VariantCalls; VariantsMerge } from "${workflow.projectDir}/modules/var
 include { TxQuantSalmon; TxQuantKallisto } from "${workflow.projectDir}/modules/pseudoalignment"
 include { Coverage; WigToBigWig; MeanCoverage; CoverageObjects; ExpressedRegions } from "${workflow.projectDir}/modules/coverage"
 include { PreprocessInputs } from "${workflow.projectDir}/modules/preprocess_inputs"
-include { PreprocessInputs } from "${workflow.projectDir}/modules/feature_counts"
+include { FeatureCounts } from "${workflow.projectDir}/modules/feature_counts"
 include { CountObjects } from "${workflow.projectDir}/modules/count_objects"
 
 workflow {

modules/quality_control/main.nf

@@ -2,6 +2,14 @@
 // workflow. In particular, it includes 'Trimming', FastQC before and after
 // trimming, and ERCC quantification
 
+def get_file_ext(f) {
+    if (f.name.toString().tokenize(".")[-1] == "gz") {
+        return('.fastq.gz')
+    } else {
+        return('.fastq')
+    }
+}
+
 /*
  * Perform FastQC on the untrimmed reads, as an initial quality gauge
  */