meryl experimental tip

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}
 		"""