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Snakefile.smk
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Snakefile.smk
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#####################################################################
## Snakefile.smk
##
## Raymond Wan ([email protected])
##
## Department of Medicine and Therapeutics,
## Division of Endocrinology & Diabetes,
## The Chinese University of Hong Kong, Hong Kong
##
## Copyright (C) 2019, Raymond Wan, All rights reserved.
#####################################################################
from snakemake.utils import validate, min_version
## Set the minimum snakemake version
min_version("5.7")
## Define global constraints on wildcards
wildcard_constraints:
topn = "\d+",
winsize = "\d+",
sample = "\w+",
method = "upstream|downstream"
## Include additional functions and rules
include: "rules/global-vars.smk"
include: "rules/other-rules.smk"
## Set the shell and the prefix to run before "shell" commands -- activate the conda environment
shell.executable ("/bin/bash")
shell.prefix ("source /opt/miniconda3/etc/profile.d/conda.sh; conda activate sam2irs; ")
## Top-level rule
rule all:
input:
OUTPUT_DIR + "/Complete/ASC_50_1000.done",
OUTPUT_DIR + "/Complete/DEK_50_1000.done",
OUTPUT_DIR + "/Complete/fSC_50_1000.done",
OUTPUT_DIR + "/Complete/pSC_50_1000.done",
OUTPUT_DIR + "/Complete/uSC_50_1000.done",
OUTPUT_DIR + "/Complete/YFP_50_1000.done",
OUTPUT_DIR + "/Complete/ASC_100_1000.done",
OUTPUT_DIR + "/Complete/DEK_100_1000.done",
OUTPUT_DIR + "/Complete/fSC_100_1000.done",
OUTPUT_DIR + "/Complete/pSC_100_1000.done",
OUTPUT_DIR + "/Complete/uSC_100_1000.done",
OUTPUT_DIR + "/Complete/YFP_100_1000.done",
OUTPUT_DIR + "/Complete/ASC_200_1000.done",
OUTPUT_DIR + "/Complete/DEK_200_1000.done",
OUTPUT_DIR + "/Complete/fSC_200_1000.done",
OUTPUT_DIR + "/Complete/pSC_200_1000.done",
OUTPUT_DIR + "/Complete/uSC_200_1000.done",
OUTPUT_DIR + "/Complete/YFP_200_1000.done",
OUTPUT_DIR + "/Complete/ASC_400_1000.done",
OUTPUT_DIR + "/Complete/DEK_400_1000.done",
OUTPUT_DIR + "/Complete/fSC_400_1000.done",
OUTPUT_DIR + "/Complete/pSC_400_1000.done",
OUTPUT_DIR + "/Complete/uSC_400_1000.done",
OUTPUT_DIR + "/Complete/YFP_400_1000.done",
OUTPUT_DIR + "/Complete/ASC_50_500.done",
OUTPUT_DIR + "/Complete/DEK_50_500.done",
OUTPUT_DIR + "/Complete/fSC_50_500.done",
OUTPUT_DIR + "/Complete/pSC_50_500.done",
OUTPUT_DIR + "/Complete/uSC_50_500.done",
OUTPUT_DIR + "/Complete/YFP_50_500.done",
OUTPUT_DIR + "/Complete/ASC_100_500.done",
OUTPUT_DIR + "/Complete/DEK_100_500.done",
OUTPUT_DIR + "/Complete/fSC_100_500.done",
OUTPUT_DIR + "/Complete/pSC_100_500.done",
OUTPUT_DIR + "/Complete/uSC_100_500.done",
OUTPUT_DIR + "/Complete/YFP_100_500.done",
OUTPUT_DIR + "/Complete/ASC_200_500.done",
OUTPUT_DIR + "/Complete/DEK_200_500.done",
OUTPUT_DIR + "/Complete/fSC_200_500.done",
OUTPUT_DIR + "/Complete/pSC_200_500.done",
OUTPUT_DIR + "/Complete/uSC_200_500.done",
OUTPUT_DIR + "/Complete/YFP_200_500.done",
OUTPUT_DIR + "/Complete/ASC_400_500.done",
OUTPUT_DIR + "/Complete/DEK_400_500.done",
OUTPUT_DIR + "/Complete/fSC_400_500.done",
OUTPUT_DIR + "/Complete/pSC_400_500.done",
OUTPUT_DIR + "/Complete/uSC_400_500.done",
OUTPUT_DIR + "/Complete/YFP_400_500.done",
OUTPUT_DIR + "/Complete/ASC_50_250.done",
OUTPUT_DIR + "/Complete/DEK_50_250.done",
OUTPUT_DIR + "/Complete/fSC_50_250.done",
OUTPUT_DIR + "/Complete/pSC_50_250.done",
OUTPUT_DIR + "/Complete/uSC_50_250.done",
OUTPUT_DIR + "/Complete/YFP_50_250.done",
OUTPUT_DIR + "/Complete/ASC_100_250.done",
OUTPUT_DIR + "/Complete/DEK_100_250.done",
OUTPUT_DIR + "/Complete/fSC_100_250.done",
OUTPUT_DIR + "/Complete/pSC_100_250.done",
OUTPUT_DIR + "/Complete/uSC_100_250.done",
OUTPUT_DIR + "/Complete/YFP_100_250.done",
OUTPUT_DIR + "/Complete/ASC_200_250.done",
OUTPUT_DIR + "/Complete/DEK_200_250.done",
OUTPUT_DIR + "/Complete/fSC_200_250.done",
OUTPUT_DIR + "/Complete/pSC_200_250.done",
OUTPUT_DIR + "/Complete/uSC_200_250.done",
OUTPUT_DIR + "/Complete/YFP_200_250.done",
OUTPUT_DIR + "/Complete/ASC_400_250.done",
OUTPUT_DIR + "/Complete/DEK_400_250.done",
OUTPUT_DIR + "/Complete/fSC_400_250.done",
OUTPUT_DIR + "/Complete/pSC_400_250.done",
OUTPUT_DIR + "/Complete/uSC_400_250.done",
OUTPUT_DIR + "/Complete/YFP_400_250.done"
rule Combine_Results:
input:
input_fn1 = OUTPUT_DIR + "/motif/{sample}/{topn}/{winsize}/upstream/dreme.html",
input_fn2 = OUTPUT_DIR + "/motif/{sample}/{topn}/{winsize}/downstream/dreme.html",
input_fn3 = OUTPUT_DIR + "/motif/{sample}/{topn}/intron/dreme.html"
output:
output_fn1 = OUTPUT_DIR + "/Complete/{sample}_{winsize}_{topn}.done"
shell:
"""
touch {output.output_fn1}
"""