Commit 85210b13 authored by sgriep's avatar sgriep
Browse files

Merge branch 'fix_reference_dir' into 'main'

fix reference directory name in rules

See merge request ahoek/wasp_sven_test!1
parents 6681c791 9005151f
......@@ -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",
......
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