WIP: Checkpoint snakefile

rules/ANALYSIS_RULES

@@ -183,7 +183,8 @@ rule minced:
     shell:
         """
         (date &&\
-        ./minced {input} {output.mn1} {output.mn2} &&\
+        export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/ &&\
+        minced {input} {output.mn1} {output.mn2} &&\
         echo $(basename -s "" {output.mn1}) >> minced_CRISPR_output.txt &&\
         grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
         date) &> >(tee {log})