From dca40749bedfdd1f424639a5db4c6d2df20a2abc Mon Sep 17 00:00:00 2001
From: Christoph Stritt <stritt0001@login01.cluster.bc2.ch>
Date: Fri, 5 Jul 2024 11:44:52 +0200
Subject: [PATCH] Duplicate read removal step added in circularize rule
---
cluster/config.yaml | 2 +-
config/config.yaml | 8 +++++---
workflow/rules/circularize.smk | 21 ++++++++++++++++++++-
3 files changed, 26 insertions(+), 5 deletions(-)
diff --git a/cluster/config.yaml b/cluster/config.yaml
index e4ec829..381cd8c 100644
--- a/cluster/config.yaml
+++ b/cluster/config.yaml
@@ -16,7 +16,7 @@ default-resources:
restart-times: 3
max-jobs-per-second: 10
max-status-checks-per-second: 1
-local-cores: 1
+local-cores: 20
latency-wait: 60
jobs: 500
keep-going: True
diff --git a/config/config.yaml b/config/config.yaml
index eb11d3b..7feb5f7 100755
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -2,8 +2,10 @@
#
##############################
-samples: config/samples.tsv
-outdir: ./results
+samples: config/samples.tsv # overwritten by run_assembly_pipeline.py
+outdir: ./results # overwritten by run_assembly_pipeline.py
+
+annotate: "No"
ref:
genome_size: 4.4m
@@ -12,7 +14,7 @@ ref:
bakta_db: /scicore/home/gagneux/GROUP/PacbioSnake_resources/databases/bakta_db
container: /scicore/home/gagneux/GROUP/PacbioSnake_resources/containers/assemblySC.sif
-threads_per_job: 4
+threads_per_job: 10 # Max. 20
assembly_iterations: 3
diff --git a/workflow/rules/circularize.smk b/workflow/rules/circularize.smk
index 89f2f78..94d3a62 100755
--- a/workflow/rules/circularize.smk
+++ b/workflow/rules/circularize.smk
@@ -24,8 +24,27 @@ rule circlator_bam2reads:
"""
+
+rule circlator_removeduplicates:
+ input: config["outdir"] +"/{sample}/circlator/02.bam2reads.fasta"
+ output: config["outdir"] +"/{sample}/circlator/02.bam2reads.nodup.fasta"
+ run:
+
+ import sys
+ from Bio import SeqIO
+
+ record_dict = {}
+
+ for record in SeqIO.parse(input[0], "fasta"):
+ record_dict[record.id] = record
+
+ # record_dict = SeqIO.to_dict(SeqIO.parse(input[0], "fasta")) # Does not allow duplicate entries...
+ with open(output[0], "w") as output_handle:
+ SeqIO.write(record_dict.values(), output_handle, "fasta")
+
+
rule circlator_localassembly:
- input: config["outdir"] + "/{sample}/circlator/02.bam2reads.fasta"
+ input: config["outdir"] + "/{sample}/circlator/02.bam2reads.nodup.fasta"
output: config["outdir"] + "/{sample}/circlator/03.assemble/assembly.fasta"
params:
outdir = config["outdir"] + "/{sample}/circlator/03.assemble",
--
GitLab