Benchmarking_paper/Makefile at master · lauringlab/Benchmarking_paper · GitHub

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#all : ./results.pdf

####################################################################################
#
#
#
#	Part 1  : Get the raw data
#
#
#
###################################################################################


#Download the fastq files for


data/raw/2014-5-30/%.fastq: data/raw/2014-5-30/SraRunInfo.csv
	./scripts/get_fastq.sh data/raw/2014-5-30/SraRunInfo.csv data/raw/2014-5-30/
	python scripts/change_names_sra.py -s data/raw/2014-5-30/ -f data/raw/2014-5-30/ -k data/raw/2014-5-30/SraRunInfo.csv -run
data/raw/2015-6-23/%.fastq: data/raw/2015-6-23/SraRunInfo.csv
	./scripts/get_fastq.sh data/raw/2015-6-23/SraRunInfo.csv data/raw/2015-6-23/
	python scripts/change_names_sra.py -s data/raw/2015-6-23/ -f data/raw/2015-6-23/ -k data/raw/2015-6-23/SraRunInfo.csv -run
data/raw/2015-11-14/%.fastq: data/raw/2015-11-14/SraRunInfo.csv
	./scripts/get_fastq.sh data/raw/2015-11-14/SraRunInfo.csv data/raw/2015-11-14/
	python scripts/change_names_sra.py -s data/raw/2015-11-14/ -f data/raw/2015-11-14/ -k data/raw/2015-11-14/SraRunInfo.csv -run


#####################################################################################
#
#
#
#	Part 2  : Primary analysis - alignment, processing, and variant calling
#		This section relies heavily on a variant calling pipeline developed
#		in Bpipe. It requires Bowtie2 and DeepSNV. The pipeline can be
#		downloaded from https://github.com/lauringlab/variant_pipeline.git.
#		The following commonands expect the variant_pipeline directory to be
#		in your home directory.
#
#
#
#######################################################################################


./data/process/2014-5-30/Variants/all.sum.csv: data/raw/2014-5-30/*.fastq
	python ~/variant_pipeline/bin/variantPipeline.py -i ./data/raw/2014-5-30/ -o ./data/process/2014-5-30/ -r ./data/reference/pHW2000_PR8-N_A -p Pr8_control -d one.sided -m fisher -a 0.9

./data/process/2015-6-23/Variants/all.sum.csv: data/raw/2015-6-23/*.fastq
	python ~/variant_pipeline/bin/variantPipeline.py -i ./data/raw/2015-6-23/ -o ./data/process/2015-6-23/ -r ./data/reference/wsn33_wt_plasmid -p Plasmid_control -d two.sided -m fisher -a 0.9
./data/process/2015-11-14/Variants/all.sum.csv: data/raw/2015-11-14/*.fastq
	python ~/variant_pipeline/bin/variantPipeline.py -i ./data/raw/2015-11-14/ -o ./data/process/2015-11-14/ -r ./data/reference/wsn33_wt_plasmid -p WSN33_Plasmid_control.dups -d two.sided -m fisher -a 0.9

./data/process/2015-6-23.one.sided/Variants/all.sum.csv:./data/process/2015-6-23/Variants/all.sum.csv
	python ~/variant_pipeline/bin/variantPipeline.py -i ./data/process/2015-6-23/04_removed_duplicates/ -o ./data/process/2015-6-23.one.sided/ -r ./data/reference/wsn33_wt_plasmid -p Plasmid_control -d one.sided -m fisher -a 0.9 -bam

./data/process/2015-6-23/Lofreq/lofreq_vcf/all.lofreq.csv: ./data/process/2015-6-23/Variants/all.sum.csv
	~/variant_pipeline/lib/bpipe-0.9.8.7/bin/bpipe run -n 3 ./scripts/lowfreq.bpipe.groovy ./data/process/2015-6-23/04_removed_duplicates/*.bam


#####################################################################################
#
#
#
#	Part 3 : Secondary analysis make the figures!
#
#
#
#####################################################################################


./results/figures.md:
	cd ./results/ ; Rscript -e "knitr::knit('./figures.Rmd')"