WIP: Checkpoint snakefile

2019_GDB/rules/ANALYSIS_RULES

@@ -168,7 +168,7 @@ 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.cas1}) >> {output.cas2} &&\
+        echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
         awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
         date) &> >(tee {log})
         """
@@ -186,7 +186,7 @@ rule minced:
         (date &&\
         export PATH=$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 &&\
+        echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
         grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
         date) &> >(tee {log})
         """