fixed errors

workflow_zymo/Snakefile

@@ -263,6 +263,11 @@ rule sibeliaz:
     log:
         out="logs/sibeliaz.{rtype1}.{tool1}.{rtype2}.{tool2}.out.log",
         err="logs/sibeliaz.{rtype1}.{tool1}.{rtype2}.{tool2}.err.log"
+    threads:
+        config["sibeliaz"]["threads"]
+    params:
+        kmers=config["sibeliaz"]["kmer"],
+        memory=config["sibeliaz"]["mem"]
     wildcard_constraints:
         rtype1="|".join(READ_TYPES),
         rtype2="|".join(READ_TYPES),
@@ -274,5 +279,5 @@ rule sibeliaz:
         "Genome comparision: Sibeliaz: {input.asm1} {input.asm2}"        
     shell:
        "(date && "
-       "sibeliaz -t config[sibeliaz][threads] -k config[sibeliaz][kmer] -f config[threads][mem] -o $(dirname {output}) {input.asm1} {input.asm2} && "
+       "sibeliaz -t {threads} -k {params.kmers} -f {params.memory} -o $(dirname {output}) {input.asm1} {input.asm2} && "
        "date) 2> {log.err} > {log.out}"        
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