Change output of diffPeaks design file.

workflow/main.nf

 #!/usr/bin/env nextflow
+test = Channel
+.fromPath('/work/BICF/s163035/builds/932983dd/2/BICF/Astrocyte/chipseq_analysis/work/ce/59578d09be684276dca671e1aea716/unique_experiments.csv')
+.splitCsv(sep: '\t', header: true)
+                      .toList()
+
+println test.size()
+
 
 // Path to an input file, or a pattern for multiple inputs
 // Note - $baseDir is the location of this workflow file main.nf
@@ -429,12 +436,8 @@ process motifSearch {
 }
 
 // Define channel to find number of unique experiments
-noUniqueExperiments = uniqueExperiments
+uniqueExperimentsList = uniqueExperiments
                       .splitCsv(sep: '\t', header: true)
-                      .toList()
-                      .count()
-
-println noUniqueExperiments
 
 // Calculate Differential Binding Activity
 process diffPeaks {
@@ -444,6 +447,7 @@ process diffPeaks {
   input:
 
   file designDiffPeaks
+  val noUniqueExperiments from uniqueExperimentsList.count()
 
   output:
 

workflow/scripts/overlap_peaks.py

@@ -212,8 +212,8 @@ def main():
     design_anno.to_csv("design_annotatePeaks.tsv", header=True, sep='\t', index=False)
 
     # Write the unique conditions
-    unique_experiments = pd.Series(design_diff['Condition'].unique)
-    unique_experiments.to_csv('unique_experiments.csv')
+    unique_experiments = pd.DataFrame(design_diff['Condition'].unique().tolist(), columns=['Condition'])
+    unique_experiments.to_csv('unique_experiments.csv', index=False)
 
 
 if __name__ == '__main__':