Merge branch 'fix_reference_dir' into 'main'

fix reference directory name in rules

See merge request ahoek/wasp_sven_test!1

Snakefile

@@ -18,7 +18,7 @@ for f in os.listdir('Samples/'):
                 SAMPLES.append(name[0])
 
 
-# Reading-in reference files from Reference directory
+# Reading-in reference files from Samples directory
 for ref in os.listdir('Samples/'):
 	if ref.endswith(".gtf"):
 		r = os.path.splitext(ref)
@@ -93,7 +93,7 @@ rule fastqc:
 # Generating genome indexes for mapping with STAR
 rule indexingMapping:
 	input:
-		fna=expand("Reference/{ref}.fa", ref=REFFA)
+		fna=expand("Samples/{ref}.fa", ref=REFFA)
 	output:
 		directory("Temporary/STAR_Indices/")
 	benchmark:
@@ -125,7 +125,7 @@ rule mapping:
 # Counting reads to genomic features with featureCounts
 rule featureCounts:
 	input:
-		gtf=expand("Reference/{ref}.gtf", ref=REFGTF),
+		gtf=expand("Samples/{ref}.gtf", ref=REFGTF),
 		bam="Temporary/{genes}/STAR_Mapping/{genes}_Aligned.sortedByCoord.out.bam"
 	output:
 		"Temporary/{genes}/featureCounts/{genes}_Aligned.sortedByCoord.out.bam.featureCounts.bam",