From 83c8980a9f77487acc65dccd52f0021c365102af Mon Sep 17 00:00:00 2001
From: "christoph.stritt@unibas.ch" <christoph.stritt@unibas.ch>
Date: Tue, 16 Jan 2024 11:46:23 +0100
Subject: [PATCH] added polishing iterations parameter for flye
---
assembly/config/config.yaml | 2 ++
assembly/workflow/rules/assemble.smk | 4 +++-
variantcalling/workflow/Snakefile | 3 ++-
3 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/assembly/config/config.yaml b/assembly/config/config.yaml
index 9af1c0c..eb11d3b 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 90d09ff..64fa1af 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 0b62ac0..d344417 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"
--
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