diff --git a/assembly/config/config.yaml b/assembly/config/config.yaml
index 9af1c0c7665a69956f1adacc03fa354521e44d4d..eb11d3bea3047d9be05641541f294eb53ad152b0 100755
--- a/assembly/config/config.yaml
+++ b/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"
diff --git a/assembly/workflow/rules/assemble.smk b/assembly/workflow/rules/assemble.smk
index 90d09fffe560fddd717c65c2a13874bebe025423..64fa1af9bef3385e2d7c310300081a71dd285c79 100755
--- a/assembly/workflow/rules/assemble.smk
+++ b/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}
     """
diff --git a/variantcalling/workflow/Snakefile b/variantcalling/workflow/Snakefile
index 0b62ac0878a1ace7c0f2a735bcff299584bb61b0..d34441723023f942ef45e385f91c99c09b61d2b1 100755
--- a/variantcalling/workflow/Snakefile
+++ b/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"