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Snakefile
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Snakefile
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import pandas as pd
import yaml, os
from snakemake.utils import validate, min_version
# set minimum snakemake version to the version its developed on
min_version("5.3.1")
# load config and mastersheet
configfile: "config.yaml"
#validate(config,schema="schemas/config.schema.yaml")
units = pd.read_csv('metasheet.csv',comment='#')
# force strings
units['RunName'] = units['RunName'].astype(str)
units['Tumor'] = units['Tumor'].astype(str)
units['Normal'] = units['Normal'].astype(str)
units = units.set_index('RunName')
# define the group wildcard
group = units.index
#validate(units,schema="schemas/units.schema.yaml")
# read our reference files
ref_vars = yaml.load(open(config['ref']).read())['ref']
# target rules
rule all:
input:
"results/annotated_variants/merged.maf"
# Modules
include: "rules/align.smk"
include: "rules/variant_calling.smk"
include: "rules/variant_annotation.smk"