WIP: Checkpoint snakefile

2019_GDB/rules/ANALYSIS_RULES

@@ -157,21 +157,19 @@ rule casc:
     input:
         os.path.join(RESULTS_DIR, "assembly/{assembly}.fa")
     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")
+        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"
     shell:
         """
-        (date &&\
-        export PATH={config[CASC][PATH]} &&\ 
-        export PERL5LIB={config[CASC][PERL5LIB]} &&\
-        casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
-        echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
-        cat {output.cas1}) | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> {output.cas2} &&\        
-        date) &> >(tee {log})
+        export PATH={config[CASC][PATH]}
+        export PERL5LIB={config[CASC][PERL5LIB]} 
+        casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative 
+        echo $(basename -s ".results.txt" {output.cas1}) >> results/analysis/crispr/casc/casc_CRISPR_output.txt 
+        cat {output.cas1} | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> results/analysis/crispr/casc/casc_CRISPR_output.txt 
         """
 
 rule minced:
@@ -187,8 +185,8 @@ rule minced:
         (date &&\
         export PATH={config[minced][PATH]} &&\
         minced {input} {output.mn1} {output.mn2} &&\
-        echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
-        grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
+        echo $(basename -s ".txt" {output.mn1}) >> results/analysis/crispr/minced/minced_CRISPR_output.txt &&\
+        grep -c 'CRISPR' {output.mn1} >> results/analysis/crispr/minced/minced_CRISPR_output.txt &&\
         date) &> >(tee {log})
         """