Commit f4b84729 authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete dada2.smk

parent 0c08a3d1
rule dada2:
input:
"work/filter/{sample}.fastq.gz"
output:
"work/dada/{sample}.rds"
threads:
config["THREADS"]
script:
"dada2.R"
rule makeSequenceTable:
input:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
rds = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta",
tsv = "work/dada/seqtab.tsv",
biom = "work/dada/dada.biom"
threads:
config["THREADS"]
script:
"makeSequenceTable.R"
rule metrics:
input:
rds = "work/dada/seqtab.rds",
fastqc = expand("work/fastqc/{sample}_fastqc.zip", sample=SAMPLES)
output:
tsv = "work/dada/metrics.tsv"
script:
"metrics.R"
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