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ReinV / SCOPE

Search and Chemical Ontology Plotting Environment
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Add executable workflows? #59

Open magnuspalmblad opened 2 years ago

magnuspalmblad commented 2 years ago

Would it make sense to add one or more executable workflows, perhaps in different workflow languages (KNIME, CWL, NextFlow, Snakemake)?

I am thinking something like this, using our favorite examples (this is executable from the Anaconda Prompt on Windows):

python download_files.py
echo 'APCI, METHODS:"atmospheric pressure chemical ionization" AND FIRST_PDATE:[20220101 TO 20221231]' > queries\workflow_query.csv
echo 'HILIC, METHODS:"hydrophilic interaction liquid chromatography" AND FIRST_PDATE:[20220101 TO 20221231]' >> queries\workflow_query.csv
python search_query.py -i queries\workflow_query.csv
python make_table.py -i results -t folder
python visualize_multiplot.py -i tables -o QUERY