final SibeliaZ rule updated

config/Zymo/config.zymo.yaml

@@ -21,4 +21,10 @@ prodigal:
     threads: 12
     
 diamond:
-    threads: 20
\ No newline at end of file
+    threads: 20
+
+# Comparison tools
+sibeliaz:
+    threads: 24
+    kmer: 25
+    mem: 2

config/Zymo/sbatch.zymo.sh

@@ -42,6 +42,6 @@ snakemake -s ${ONTP_SMK} -rp --jobs 10 --local-cores 1 \
  --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}" --unlock 
  
 # run the pipeline
-snakemake -s ${ONTP_SMK} -rpn --jobs 10 --local-cores 1 \
+snakemake -s ${ONTP_SMK} -rp --jobs 10 --local-cores 1 \
  --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
  --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"

workflow_zymo/Snakefile

@@ -75,9 +75,7 @@ rule all:
         expand(os.path.join(RESULTS_DIR, "analysis/comparison/{rtype_tool}_comparison.txt"), 
             rtype_tool=["%s_%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]),
          expand(os.path.join(RESULTS_DIR, "analysis/sibeliaz/{combi}_output/blocks_coords.gff"),
-            combi=["%s_%s__%s_%s" % (p[0][0], p[0][1], p[1][0], p[1][1]) for p in READ_ASSEMBLER_PAIRS] +
-            ["%s_%s__%s_%s" % (p[1][0], p[1][1], p[0][0], p[0][1]) for p in READ_ASSEMBLER_PAIRS])
-            
+            combi=["%s_%s__%s_%s" % (p[0][0], p[0][1], p[1][0], p[1][1]) for p in READ_ASSEMBLER_PAIRS])
 
 rule download_genomes:
     output: