edited the to fix the snakemake error - try # 14 million and one

2019_GDB/rules/ANALYSIS_RULES

@@ -159,6 +159,7 @@ rule casc:
     output:
         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")
+#        cas3=directory(os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output"))
     log: os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc.log")
     threads: config["mmseq2"]["threads"]
     conda: "../envs/analysis.yaml"
@@ -169,7 +170,6 @@ rule casc:
         export PERL5LIB={config[CASC][PERL5LIB]} &&\
         casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
         echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
-#        awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
         cat {output.cas1}) | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> {output.cas2} &&\        
         date) &> >(tee {log})
         """

rules/ANALYSIS_RULES

@@ -159,6 +159,7 @@ rule casc:
     output:
         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")
+#        cas3=directory(os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output"))
     log: os.path.join(RESULTS_DIR, "analysis/crispr/casc/{assembly}_casc_output/casc.log")
     threads: config["mmseq2"]["threads"]
     conda: "../envs/analysis.yaml"
@@ -169,7 +170,6 @@ rule casc:
         export PERL5LIB={config[CASC][PERL5LIB]} &&\
         casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
         echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
-#        awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
         cat {output.cas1}) | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> {output.cas2} &&\        
         date) &> >(tee {log})
         """