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ahoek
wasp_sven_test
Commits
85210b13
Commit
85210b13
authored
Nov 12, 2021
by
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
Changes
1
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85210b13
...
...
@@ -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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