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Snakefile
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##########################################################################################
# ___ ___ ___ ___ ___ ___ #
# /\ \ /\__\ /\__\ /\__\ ___ /\__\ /\ \ #
# /::\ \ /:/ / /:/ / /::| | /\ \ /::| | /::\ \ #
# /:/\:\ \ /:/ / /:/ / /:|:| | \:\ \ /:|:| | /:/\:\ \ #
# /::\~\:\ \ /:/ / /:/ / /:/|:|__|__ /::\__\ /:/|:| |__ /::\~\:\ \ #
# /:/\:\ \:\__\ /:/__/ /:/__/ /:/ |::::\__\ __/:/\/__/ /:/ |:| /\__\ /:/\:\ \:\__\#
# \/__\:\/:/ / \:\ \ \:\ \ \/__/~~/:/ / /\/:/ / \/__|:|/:/ / \:\~\:\ \/__/#
# \::/ / \:\ \ \:\ \ /:/ / \::/__/ |:/:/ / \:\ \:\__\ #
# /:/ / \:\ \ \:\ \ /:/ / \:\__\ |::/ / \:\ \/__/ #
# /:/ / \:\__\ \:\__\ /:/ / \/__/ /:/ / \:\__\ #
# \/__/ \/__/ \/__/ \/__/ \/__/ \/__/ #
##########################################################################################
# AllMine, a flexible pipeline for Allele Mining #
# This software is under the MIT License #
# Copyright Thomas Bersez 2019 #
# INRA-GAFL / Paris Saclay university #
# contact: [email protected] #
# This Snakefile script controls the loading and execution of the different
# modules/<name>.py. It is use to start the AllMine pipeline.
# The "config.yaml" file, generated by csv_to_yaml.py, must be present in the
# working directory.
# Several directories containing, processed reads, bam and putative variants
# will be created in the working directory by the pipeline.
# Make sure that you have the needed rights, space and resources
# where you run AllMine!
configfile: "config.yaml"
cwd = os.getcwd() + "/"
# modules loading...
include : cwd + "modules/" + config["QC"]
include : cwd + "modules/" + config["FASTP"]
include : cwd + "modules/" + config["INDEXER"]
include : cwd + "modules/" + config["ALLIGNER"]
include : cwd + "modules/bam_with_bed_parse.py"
include : cwd + "modules/cov_tracks.py"
include : cwd + "modules/vcf_to_avinput.py"
include : cwd + "modules/varscan.py"
include : cwd + "modules/annovar.py"
include : cwd + "modules/make_report.py"
include : cwd + "modules/bam_index.py"
include : cwd + "modules/whatshap.py"
include : cwd + "modules/do_markdown.py"
# target files...
#
# expand(config["VAR"] + "{samples}/{samples}_varscan_phased.vcf", samples = config["samples"])
# - This line is used to ask for trying to phase SNPs, note that phasing is efficient for
# at least 10X 300bp paired end. No errors will be returned if the phasing fail !
# Browse the outputs to get the results.
rule all:
input:
expand(config["VAR"] + "{samples}/{samples}_varscan_phased.vcf", samples = config["samples"]),
"Run_report.html"