viloca dname_work as params

cbg-ethz · Jun 11, 2024 · 30ab9ce · 30ab9ce
1 parent 732c9eb
commit 30ab9ce
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/rsv_wastewater/workflow/Snakefile b/rsv_wastewater/workflow/Snakefile
@@ -136,16 +136,16 @@ rule run_viloca:
     output:
         fname_vcf=f"results/{{sample}}/snvs.vcf",
         fname_csv=f"results/{{sample}}/variant_calling/snv/cooccurring_mutations.csv",
-        dname_work=directory(
-            f"results/{{sample}}/variant_calling/"
-        ),
         dname_haplotypes=directory(
             f"results/{{sample}}/variant_calling/support/"
         ),
     benchmark:
         f"results/{{sample}}/benchmark.tsv"
     params:
-        sample= lambda wc: wc.get("sample")
+        sample= lambda wc: wc.get("sample"),
+        dname_work=directory(
+            f"results/{{sample}}/variant_calling/"
+        ),
     conda:
         "envs/viloca.yaml"
     threads: 30,

diff --git a/rsv_wastewater/workflow/scripts/run_viloca.py b/rsv_wastewater/workflow/scripts/run_viloca.py
@@ -55,7 +55,7 @@ def main(fname_bam, fname_reference, fname_insert_bed, fname_results_snv, dname_
         Path(snakemake.input.fname_reference),
         Path(snakemake.input.fname_insert_bed),
         Path(snakemake.output.fname_vcf),
-        Path(snakemake.output.dname_work),
+        Path(snakemake.params.dname_work),
         snakemake.params.sample,
         snakemake.threads
     )