MakefileFastq_compare

# This Makefile runs several times sickles, our script gather before and after information about the trimming to help the user choose proper parameter to do the trimming
# Rule 'all' which is a make keyword
all: global_report.txt

# Another keyword, used to 
clean:
	rm -f *temp.txt

# Step1: Run Sickle parameter set1
output_fastq_set1.fastqsanger: test/in.fastq
	../sickle/sickle se -f test/in.fastq -t sanger -o output_fastq_set1.fastqsanger -q 13 -l 40
# Step2: run our python script fastq_compare
report_set1_temp.txt: test/in.fastq output_fastq_set1.fastqsanger
	./fastq_compare.py test/in.fastq output_fastq_set1.fastqsanger phred33 report_set1_temp.txt

# Step3: Run Sickle parameter set2
output_fastq_set2.fastqsanger: test/in.fastq
	../sickle/sickle se -f test/in.fastq -t sanger -o output_fastq_set2.fastqsanger -q 39 -l 40
# Step4: run our python script fastq_compare
report_set2_temp.txt: test/in.fastq output_fastq_set2.fastqsanger
	./fastq_compare.py test/in.fastq output_fastq_set2.fastqsanger phred33 report_set2_temp.txt



# step5
global_report.txt: report_set1_temp.txt report_set2_temp.txt
	more report_set*_temp.txt > global_report.txt