Get the assembler variable parsed out by snakemake directly

Note the missing single quotes around the variable wrapped by square
brackets {config[foo]} .

Thanks to @tomas-pluskal for the link to
https://stackoverflow.com/questions/49140578/how-can-one-access-snakemake-config-variables-inside-shell-section

Snakefile

@@ -474,8 +474,7 @@ Runs Trinity script to get statistics about the assembled transcriptome
     1
   shell:
     """
-    assembler=$( grep '^assembler: ' config.yaml | sed -e 's/^assembler: "\(.*\)"/\1/' )
-    if [ "$assembler" -eq 'trinity' ]; then
+    if [ {config[assembler]} -eq 'trinity' ]; then
         {TRINITY_HOME}/util/TrinityStats.pl {input.transcriptome} > {output.stats} 2> {log}
     else
         {TRINITY_HOME}/util/TrinityStats.pl {input.transcriptome} | sed -e 's/trinity/rnaspades/g' > {output.stats} 2> {log}