diff --git a/rules/rulesNew.smk b/rules/rulesNew.smk index 9e63103bca5fac99ca5b795c560001b16a8690e3..b7835de48507a3dabe5a998076686c7941086b60 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} """