added polishing iterations parameter for flye

assembly/config/config.yaml

@@ -14,4 +14,6 @@ container: /scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/assembly
 
 threads_per_job: 4
 
+assembly_iterations: 3
+
 keep_intermediate: "Yes"

assembly/workflow/rules/assemble.smk

@@ -7,13 +7,15 @@ rule flye:
   threads: config["threads_per_job"]
   params:
     genome_size = config["ref"]["genome_size"],
-    outdir = config["outdir"] + "/{sample}/flye"
+    outdir = config["outdir"] + "/{sample}/flye",
+    iterations = config["assembly_iterations"]
 
   shell:
     """
     flye \
       --pacbio-hifi {input} \
       --genome-size {params.genome_size} \
+      --iterations {params.iterations} \
       --threads {threads} \
       --out-dir {params.outdir}
     """

variantcalling/workflow/Snakefile

@@ -28,7 +28,7 @@ rule combine_assemblies:
 rule pggb:
     input: config["outdir"] + "/single_contig_assemblies.fasta"
     output: config["outdir"] + "/graph.smooth.final.gfa"
-    threads: 20
+    threads: config["threads"]
     params:
         nr_strains = len(samples),
         outdir = config["outdir"],
@@ -54,6 +54,7 @@ rule pggb:
 rule call_variants:
     input: config["outdir"] + "/graph.smooth.final.gfa"
     output: config["outdir"] + "/variants.vcf"
+    threads: config["threads"]
     params:
         reference = config["reference"]
     singularity: "container/pggb_latest.sif"