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Snakefile
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Snakefile
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import snakemake.utils # Load snakemake API
import sys # System related operations
# Python 3.7 is required
if sys.version_info < (3, 7):
raise SystemError("Please use Python 3.7 or later.")
# Snakemake 5.4.2 at least is required
snakemake.utils.min_version("5.4.2")
include: "rules/common.smk"
include: "rules/copy.smk"
include: "rules/fastqc.smk"
include: "rules/multiqc.smk"
include: "rules/kallisto.smk"
include: "rules/aggregation.smk"
workdir: config["workdir"]
singularity: config["singularity_docker_image"]
localrules: copy_fastq, copy_extra
rule all:
input:
**targets_dict
message:
"Finishing the Kallisto RNA-Seq quantification pipeline"