fixing some errors after merging pull request

README.md

@@ -44,9 +44,9 @@ In order to use the workflow you need to:
                 --assess_dir			Dir where the data for the benchmark are stored
 
 	    Other options:
-                --validation_result		The output directory where the results from validation step will be saved
-				--assessment_results	The output directory where the results from the computed metrics step will be saved
-				--aggregation_results	The output directory where the consolidation of the benchmark will be saved
+                --validation_result		The output file where the results from validation step will be saved
+				--assessment_results	The output file where the results from the computed metrics step will be saved
+				--aggregation_results	The output file where the consolidation of the benchmark will be saved
 				--statistics_results	The output directory with nextflow statistics
 				--outdir	The output directory where the consolidation of the benchmark will be saved
 				--statsdir	The output directory with nextflow statistics

main.nf

@@ -76,7 +76,7 @@ community_id = params.community_id
 validation_out = file(params.validation_result)
 assessment_out = file(params.assessment_results)
 aggregation_dir = file(params.outdir)
-data_model_export_dir = file(params.data_model_export_dir)>
+data_model_export_dir = file(params.data_model_export_dir)
 other_dir = file(params.otherdir)
 
 
@@ -136,11 +136,11 @@ process benchmark_consolidation {
 	val participant_metrics from PARTICIPANT_DATA
 	val aggregation_dir
 	val validation_out
-	val data_model_export_path
+	val data_model_export_dir
 
 	"""
 	python /app/manage_assessment_data.py -b $benchmark_data -p $participant_metrics -o $aggregation_dir
-	python /app/merge_data_model_files.py -p $validation_out -m $participant_metrics -a $aggregation_dir -o $data_model_export_path
+	python /app/merge_data_model_files.py -p $validation_out -m $participant_metrics -a $aggregation_dir -o $data_model_export_dir
 	"""
 
 }

nextflow.config

@@ -48,7 +48,7 @@ params  {
   goldstandard_dir = "$baseDir/TCGA_sample_data/metrics_ref_datasets"
 
   // cancer types for which the benchmark has to be performed
-  event_id  = "ACC BRCA"
+  challenges_ids  = "ACC BRCA"
 
   // directory where TCGA benchmarking data is found
   assess_dir = "$baseDir/TCGA_sample_data/data"
@@ -64,8 +64,6 @@ params  {
   assessment_results = "sample_out/assessment_out/Assessment_datasets.json"
   outdir = "sample_out/results"
   statsdir = "sample_out/stats"
-  validation_result = "sample_out/participant_out"
-  assessment_results = "sample_out/assessment_out"
   outdir = "sample_out/results"
   statsdir = "sample_out/stats"
   data_model_export_dir = "sample_out/benchmarking_data_model_export/consolidated_result.json"