refactored Snakefile

Snakefile

@@ -15,37 +15,23 @@ kmer_lengths = config['kmers']
 
 #kmer_lengths = [24]
 
-#Helper function that assembles required input files dependent on configuration settings
-def get_input():
-	input_list = []
-
-	if config['generative_model']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.probabilistic_gen.tsv',kmer=kmer_lengths))
-	if config['probabilistic_model']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.probabilistic_cov.tsv',kmer=kmer_lengths))
-		if config['plot_top3_fit']:
-			input_list.append(expand('data/output/'+config['input_folder']+'/kmers/{kmer}/{id}_top3fit.svg',kmer=kmer_lengths,id=inputIDs))
-	if config['distance_model']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.euclidean.tsv',kmer=kmer_lengths))
-	if config['assembly_model']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/{id}/exactMatches.tsv',id=inputIDs))
-	if config['calc_strand_bias']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/{id}/strandbias.txt',id=inputIDs))
-	if config['mapping_diff_analysis']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/methodAnalysis/{id}/mapping.comparison',id=inputIDs))
-	if config['map_filtered_reads']:
-		input_list.append(expand('data/output/'+config['input_folder']+'/methodAnalysis/{id}/alignmentToGroundTruthType.sorted.bam.bai',id=inputIDs))
-	if config['verifyUniqueness']:
-		input_list.append(expand('data/output/kmers/{kmer}/uniquenessTest.tsv',kmer=kmer_lengths))
-	if config['kmer_stats_analysis']:
-		input_list.append(expand('data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/stats.tsv',kmer=kmer_lengths,id=inputIDs))
-		input_list.append(expand('data/output/'+config['input_folder']+'/kmers/{kmer}/{id}/spaTypesGroundTruthVennDia.svg',kmer=kmer_lengths,id=inputIDs))
-
-	return input_list
+possible_params = {'generative_model': expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.probabilistic_gen.tsv',kmer=kmer_lengths),
+'probabilistic_model': expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.probabilistic_cov.tsv',kmer=kmer_lengths),
+# if above:
+'plot_top3_fit': expand('data/output/'+config['input_folder']+'/kmers/{kmer}/{id}_top3fit.svg',kmer=kmer_lengths,id=inputIDs),
+'distance_model': expand('data/output/'+config['input_folder']+'/kmers/{kmer}/predictions.euclidean.tsv',kmer=kmer_lengths),
+'assembly_model': expand('data/output/'+config['input_folder']+'/{id}/exactMatches.tsv',id=inputIDs),
+'calc_strand_bias': expand('data/output/'+config['input_folder']+'/{id}/strandbias.txt',id=inputIDs),
+'mapping_diff_analysis': expand('data/output/'+config['input_folder']+'/methodAnalysis/{id}/mapping.comparison',id=inputIDs),
+'map_filtered_reads': expand('data/output/'+config['input_folder']+'/methodAnalysis/{id}/alignmentToGroundTruthType.sorted.bam.bai',id=inputIDs),
+'verifyUniqueness': expand('data/output/kmers/{kmer}/uniquenessTest.tsv',kmer=kmer_lengths),
+'kmer_stats_analysis': expand('data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/stats.tsv',kmer=kmer_lengths,id=inputIDs) + 
+						expand('data/output/'+config['input_folder']+'/kmers/{kmer}/{id}/spaTypesGroundTruthVennDia.svg',kmer=kmer_lengths,id=inputIDs)
+}
 
 rule all:
 	input:
-		get_input()
+		[possible_params[k] for k in possible_params.keys() if config[k]]
 
 
 ##### load rules #####