Update ANALYSIS_RULES

2019_GDB/rules/ANALYSIS_RULES

@@ -157,18 +157,19 @@ rule casc:
     input:
         os.path.join(RESULTS_DIR, "assembly/{assembly}.fa")
     output:
-        os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt")
+        cas1=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/{assembly}.results.txt"),
+        cas2=os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc_CRISPR_output.txt")
     log: os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc.log")
     threads: config["mmseq2"]["threads"]
     conda: "../envs/analysis.yaml"
     shell:
         """
         (date &&\
-        export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\ 
+        export PATH=$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}) -n 12 --conservative &&\
-        echo $(basename -s "" {output}) >> casc_CRISPR_output.txt &&\
-        awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output} >> casc_CRISPR_output.txt &&\
+        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} &&\
         date) &> >(tee {log})
         """