Makefile

test:
	python ./bin/main.py test_data/Cholesterol_130uM_GB1_01_6914.mzXML output_dir

test_workflow:
	nextflow run extract_data.nf \
	--outdir="./nf_test" \
	-resume	

test_cluster_Chemicalstandards:
	nextflow run extract_data.nf -c cluster.config \
	--inputSpectra="/data/massive/MSV000078556/ccms_peak/Chemicalstandards/*" \
	--outdir="./nf_Chemicalstandards" \
	-with-trace -resume
	
# ABX 3D Mouse Plates
MSV000082048:	
	nextflow run extract_data.nf -c cluster.config \
	--inputSpectra="/data/massive/MSV000082048/peak/**.mzML" \
	--outdir="./nf_MSV000082048" \
	-with-trace -resume

# ONR Primary Rat Fecal
MSV000082582:
	nextflow run extract_data.nf -c cluster.config \
	--inputSpectra="/data/massive/MSV000082869/peak/Colgate_phase2/**.mzXML" \
	--outdir="./nf_MSV000082582" \
	-with-trace -resume

# Kawasaki Disease Positive
MSV000083388:
	nextflow run extract_data.nf -c cluster.config \
	--inputSpectra="/data/massive/MSV000083388/peak/Positive Mode/**.mzXML" \
	--outdir="./nf_MSV000083388" \
	-with-trace -resume