outputs = {
"output": None
}
command = """
../tools/quantifier --log DEBUG --annotation ${annotation} -i ${alignment} -o ${output}
"""
if __name__ == "__main__":
pipeline = Pipeline()
# add tools to the pipeline
interleaver = pipeline.add(Interleaver())
aligner = pipeline.add(Aligner())
quantifier = pipeline.add(Quantifier())
# configure the tools
interleaver.reads = "../data/reads_1.fastq ../data/reads_2.fastq"
interleaver.output = "reads.fastq"
aligner.reads = interleaver.output
aligner.index = "../data/genome.gem"
aligner.result = "alignment.map"
quantifier.alignment = aligner.result
quantifier.annotation = "../data/genome.gtf"
quantifier.output = "counts.txt"
pipeline.validate()
pipeline.run()
