Update main.yml

lfnothias · Jan 4, 2024 · 2130122 · 2130122
1 parent 7bde358
commit 2130122
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -19,34 +19,34 @@ jobs:
 
     - name: Run vm-NAP Processing Tests
       run: |
-        python vm-NAP_processing.py 
-        python vm-NAP_processing.py --help
-        python vm-NAP_processing.py --debug --run_biotransformer --type_of_biotransformation='hgut'
-        python vm-NAP_processing.py --debug --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer
-        python vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
-        python vm-NAP_processing.py --debug --job_id False --sirius_input_file 'input/compound_identifications.tsv'
-        python vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --sirius_input_file 'input/compound_identifications.tsv'
+        python src/vm-NAP_processing.py 
+        python src/vm-NAP_processing.py --help
+        python src/vm-NAP_processing.py --debug --run_biotransformer --type_of_biotransformation='hgut'
+        python src/vm-NAP_processing.py --debug --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer
+        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
+        python src/vm-NAP_processing.py --debug --job_id False --sirius_input_file 'input/compound_identifications.tsv'
+        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --sirius_input_file 'input/compound_identifications.tsv'
     - name: Test with Extra Compounds and Custom Biotransformation Mode
       run: |
-        python vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --debug
+        python src/vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --debug
     - name: Test with GNPS Data, SyGMa, and BioTransformer
       run: |
-        python vm-NAP_processing.py --debug --run_sygma --max_compounds_debug=10 --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
+        python src/vm-NAP_processing.py --debug --run_sygma --max_compounds_debug=10 --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
     - name: Test with Full GNPS Parameters and Debug Mode
       run: |
-        python vm-NAP_processing.py --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='neg' --max_ppm_error=15 --min_cosine=0.7 --shared_peaks=4 --max_spec_charge=3 --debug --sirius_input_file 'input/compound_identifications.tsv'
+        python src/vm-NAP_processing.py --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='neg' --max_ppm_error=15 --min_cosine=0.7 --shared_peaks=4 --max_spec_charge=3 --debug --sirius_input_file 'input/compound_identifications.tsv'
     - name: Test with Extra Compounds, Custom Biotransformation, and SyGMa
       run: |
-        python vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --run_sygma --phase_1_cycle=2 --phase_2_cycle=1 --top_sygma_candidates=5 --debug
+        python src/vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --run_sygma --phase_1_cycle=2 --phase_2_cycle=1 --top_sygma_candidates=5 --debug
     - name: Test with Metadata Filtering and SIRIUS Parameters
       run: |
-        python vm-NAP_processing.py --compound_name_to_keep 'a' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.8 --confidence_score=0.2 --db_links='KEGG' --debug
+        python src/vm-NAP_processing.py --compound_name_to_keep 'a' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.8 --confidence_score=0.2 --db_links='KEGG' --debug
     - name: Test with Planar Structure and BioTransformer Standard Mode
       run: |
-        python vm-NAP_processing.py --use_planar_structure_boolean=True --run_biotransformer --mode='standard' --type_of_biotransformation='hgut' --number_of_steps=2 --debug
+        python src/vm-NAP_processing.py --use_planar_structure_boolean=True --run_biotransformer --mode='standard' --type_of_biotransformation='hgut' --number_of_steps=2 --debug
     - name: Test with All Parameters Combined
       run: |
-        python vm-NAP_processing.py --debug --max_compounds_debug=20 --run_sygma --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --max_ppm_error=10 --min_cosine=0.6 --shared_peaks=3 --max_spec_charge=2 --compound_name_to_keep 'a' --extra_compounds_table_file='input/extra_compounds.tsv' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.7 --confidence_score=0.1 --db_links='HMDB' --use_planar_structure_boolean=True --run_sygma --phase_1_cycle=1 --phase_2_cycle=1 --top_sygma_candidates=10 --run_biotransformer --mode='-k pred -b superbio -a' --type_of_biotransformation='allHuman' --number_of_steps=1 > test_output.txt
+        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --run_sygma --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --max_ppm_error=10 --min_cosine=0.6 --shared_peaks=3 --max_spec_charge=2 --compound_name_to_keep 'a' --extra_compounds_table_file='input/extra_compounds.tsv' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.7 --confidence_score=0.1 --db_links='HMDB' --use_planar_structure_boolean=True --run_sygma --phase_1_cycle=1 --phase_2_cycle=1 --top_sygma_candidates=10 --run_biotransformer --mode='-k pred -b superbio -a' --type_of_biotransformation='allHuman' --number_of_steps=1 > test_output.txt
 
     - name: Compare Output with Baseline
       run: |