From b7c6d8c8fd36bd83e6ab88a9287b117ba4feef61 Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Mon, 15 Mar 2021 17:25:49 +0100
Subject: [PATCH] meryl experimental tip
---
rules/rulesNew.smk | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk
index 9e63103..b7835de 100644
--- a/rules/rulesNew.smk
+++ b/rules/rulesNew.smk
@@ -21,7 +21,7 @@ rule trimAdapters:
output:
directory(os.path.join(config['Results'],"{sample}/0_qualityControl/01_fastqc"))
threads:
- workflow.cores * 0.5
+ 8
log:
os.path.join(config['Results'], "logs/0_qualityControl/{sample}_tGalore.log")
priority:
@@ -162,7 +162,6 @@ rule meryl_R1:
"../envs/merylMerq.yaml"
shell:
"""
- export OMP_NUM_THREADS={threads}
({params.script} count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
"""
@@ -187,7 +186,6 @@ rule meryl_R2:
"../envs/merylMerq.yaml"
shell:
"""
- export OMP_NUM_THREADS={threads}
({params.script} count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
"""
@@ -202,8 +200,7 @@ rule meryl:
# r1= "{sample}" + "_R1.21.meryl",
# r2= "{sample}" + "_R2.21.meryl",
# dB= "{sample}" + "_dB.21.meryl",
- path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/{sample}_dB.21.meryl"),
- split_threads= workflow.cores * 0.25
+ path= os.path.join(config['Results'], "{sample}" +"/2_QVstats_merylAndMerqury/{sample}_dB.21.meryl")
threads:
workflow.cores * 0.5
output:
@@ -216,7 +213,6 @@ rule meryl:
"../envs/merylMerq.yaml"
shell:
"""
- export OMP_NUM_THREADS={threads}
({params.script} union-sum {input.read1} {input.read2} threads={threads} output {output}) &> {log}
"""
--
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