Commit 95eb0173 authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete global.smk

parent f4b84729
shell.executable("/bin/bash")
shell.prefix("source /usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh;")
configfile: "./config.json"
SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.fasta",
"work/dada/seqtab.tsv",
"work/dada/metrics.tsv",
"work/FROGS/affiliation.biom",
"report/clusters_metrics.html",
"report/affiliations_metrics.html",
"report/abundance.biom",
"report/abundance.tsv",
# "report/tree.nwk"
include: "quality.smk"
include: "preprocess.smk"
include: "dada2.smk"
include: "affiliation.smk"
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