fixing relative_amplicon_coverage rule

cbg-ethz · Sep 12, 2024 · 8e804e0 · 8e804e0
1 parent cbe233f
commit 8e804e0
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/workflows/amplicon_cov.smk b/workflows/amplicon_cov.smk
@@ -12,14 +12,14 @@ primers_fp = "../resources/amplicon_cov/articV3primers.bed"
 rule relative_amplicon_coverage:
     input:
         sample_list = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples.tsv",
-        samples = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples",
+        samples = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples"
     output:
-        output_dir = output_dir+ "/cov_heatmap.pdf"
+        output_dir = output_dir + "/cov_heatmap.pdf"
     shell:
-        f"""
-        python ../scripts/amplicon_covs.py -pv /
-            -s {{input.sample_list}} /
-            -f {{input.samples}} /
-            -r articV3primers.bed /
-            -o {{output.output_dir}} /
+        """
+        python ../scripts/amplicon_covs.py \
+            -s {input.sample_list} \
+            -f {input.samples} \
+            -r articV3primers.bed \
+            -o {output.output_dir}
         """