Commit ec4a18b1 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

Update Snakefile_para_gatk_PEmerged.smk

parent 40b7f2c0
......@@ -58,7 +58,6 @@ def get_fql2(wildcards):
return ml
####################################################################################
############################ filan rule ############################################
####################################################################################
......@@ -95,7 +94,6 @@ rule fastp_pe:
R2 = "{outdir}/fastp/{{sample}}_2_trim.fastq.gz".format(outdir=config["outdir"])
message: "Running fastp on files \n"
params:
spl = config["outdir"]+"/fastp/{sample}",
fqdir = config["fq_dir"],
outdir = config["outdir"],
modules = config["MODULES"],
......@@ -106,13 +104,10 @@ rule fastp_pe:
html = config["outdir"]+"/fastp/{sample}_trim.html"
shell:
"""
date
cat {input.R1} >{params.spl}.r1.fq.tmp.gz
date
cat {input.R2} >{params.spl}.r2.fq.tmp.gz
singularity exec {params.bind} {params.fastp_bin} fastp \
-i {params.spl}.r1.fq.tmp.gz \
-I {params.spl}.r2.fq.tmp.gz \
--stdin \
-i <(zcat {input.R1}) \
-I <(zcat {input.R2}) \
-o {output.R1} \
-O {output.R2} \
-h {params.html} \
......@@ -125,8 +120,6 @@ rule fastp_pe:
--low_complexity_filter \
--complexity_threshold 30 \
-w 4
rm -f {params.spl}.r1.fq.tmp.gz {params.spl}.r2.fq.tmp.gz
rm -f {params.html} {params.json}
"""
# 1-2) merge reads for and rev :
......
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