Fixing access to params.

smwrappers/map_on_genome/wrapper.py

@@ -53,8 +53,8 @@ shell(mapping_command(snakemake.params.aligner))
 
 if hasattr(snakemake.output, "methods"):
     shell(f"cp {snakemake.input.methods} {snakemake.output.methods}")
-    methods = f"The {params.read_name} were mapped on the {params.genome_name} using {aligner} (version ${{{{v}}}}) with options {snakemake.params.settings}"
+    methods = f"The {snakemake.params.read_name} were mapped on the {snakemake.params.genome_name} using {snakemake.params.aligner} (version ${{{{v}}}}) with options {snakemake.params.settings}"
     shell(f"""
-        v=$({aligner} --version | head -1 | awk '{{print $3}}')
+        v=$({snakemake.params.aligner} --version | head -1 | awk '{{print $3}}')
         echo "{methods}" >> {snakemake.output.methods}
 """)