From 30ab9ce2202b2964b41d7e0b1a07bc1c5dc33cf1 Mon Sep 17 00:00:00 2001
From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com>
Date: Tue, 11 Jun 2024 10:02:58 +0200
Subject: [PATCH] viloca dname_work as params

---
 rsv_wastewater/workflow/Snakefile             | 8 ++++----
 rsv_wastewater/workflow/scripts/run_viloca.py | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/rsv_wastewater/workflow/Snakefile b/rsv_wastewater/workflow/Snakefile
index 108da81..76920d9 100644
--- 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
index 1e9c1a2..1aefbca 100644
--- 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
     )