WIP: Checkpoint snakefile

2019_GDB/rules/ANALYSIS_RULES

@@ -168,8 +168,8 @@ rule casc:
         export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\
         export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl
         casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
-        echo $(basename -s "" {output}) >> {output.cas2} &&\
-        awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output} >> {output.cas2} &&\
+        echo $(basename -s "" {output.cas1}) >> {output.cas2} &&\
+        awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
         date) &> >(tee {log})
         """