Commit 5f2d4bd6 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

khmer

parent 6e480a47
def khmer_input(wildcards):
if config["SORTMERNA"]:
return {"R1R2": "work/sortmerna/{wildcards.reads}_mRNA.fastq.gz".format(wildcards=wildcards)}
else:
return {"R1R2": "DATA/trim/{wildcards.reads}_R1R2.fastq.gz".format(wildcards=wildcards)}
rule khmer:
input:
unpack(khmer_input)
output:
R1R2 = "work/khmer/{reads}_R1R2.fastq.gz",
log = "work/khmer/{reads}.log"
threads:
10
params:
mem_tot = 90 * 1e9,
K = 32,
C = 100
shell:
"normalize-by-median.py "
"--ksize {params.K} "
"--max-memory-usage {params.mem_tot} "
"--cutoff {params.C} "
"--paired "
"--report {output.log} "
"--output {output.R1R2} "
"--gzip "
"{input.R1R2}"
......@@ -14,7 +14,7 @@
"khmer" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
"cluster" : "-l big_mem"
},
"megahit" :
{
......
......@@ -12,3 +12,4 @@ rule all:
include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
include: "../workflow_metagenomics/kaiju.smk"
include: "../workflow_metagenomics/assembly.smk"
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