[mg] fixed the conflicts in the Snakefile

R-ODAF · Oct 26, 2023 · fca7dda · fca7dda
1 parent 413c85f
commit fca7dda
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -413,15 +413,16 @@ if common_config["platform"] =="RNA-Seq":
             genome = genome_dir / pipeline_config["genome_filename"]
         params:
             annotations = genome_dir / pipeline_config["annotation_filename"],
-            genome_name = pipeline_config["genome_name"]
+            genome_name = pipeline_config["genome_name"],
+            genome_dir = pipeline_config["genomedir"]
         output:
             directory(genome_dir / "RSEM_index")
         conda:
             "envs/preprocessing.yml"
         benchmark: log_dir / "benchmark.RSEM_make_index.txt"
         shell:
             '''
-            mkdir RSEM_index
+            mkdir {params.genome_dir}/RSEM_index
             rsem-prepare-reference --gtf {params.annotations} {input.genome} {output}/{params.genome_name}
             '''