Commit 97f9e08b authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

paired end

parent 3b152cbc
rule dada2:
input:
filt = "work/filter/{sample}_1.fastq.gz"
filtrev = "work/filter/{sample}_2.fastq.gz"
filt = "work/filter/{sample}.sra_1.fastq.gz",
filtrev = "work/filter/{sample}.sra_2.fastq.gz"
output:
"work/dada/{sample}.rds"
threads:
......
rule cutadapt:
input:
fwd = "DATA/{sample}_1.fastq.gz"
rev = "DATA/{sample}_2.fastq.gz"
fwd = "DATA/{sample}.sra_1.fastq.gz",
rev = "DATA/{sample}.sra_2.fastq.gz"
output:
cut = "work/cutadapt/{sample}_1.fastq.gz"
cutrev = "work/cutadapt/{sample}_2.fastq.gz"
cut = "work/cutadapt/{sample}.sra_1.fastq.gz",
cutrev = "work/cutadapt/{sample}.sra_2.fastq.gz"
params:
five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
......@@ -25,10 +24,10 @@ rule cutadapt:
rule filter:
input:
cut = "work/cutadapt/{sample}_1.fastq.gz"
cutrev = "work/cutadapt/{sample}_2.fastq.gz"
cut = "work/cutadapt/{sample}.sra_1.fastq.gz",
cutrev = "work/cutadapt/{sample}.sra_2.fastq.gz"
output:
filt = "work/filter/{sample}_1.fastq.gz"
filtrev = "work/filter/{sample}_2.fastq.gz"
filt = "work/filter/{sample}.sra_1.fastq.gz",
filtrev = "work/filter/{sample}.sra_2.fastq.gz"
script:
"filterAndTrim.R"
rule fastqc:
input:
"DATA/{sample}.fastq.gz"
fwd = "DATA/{sample}.sra_1.fastq.gz",
rev = "DATA/{sample}.sra_2.fastq.gz"
output:
zip = "work/fastqc/{sample}_fastqc.zip",
html = "work/fastqc/{sample}_fastqc.html"
......
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