flow_filelinking.yaml0000644000000000000000000000161114540151521013757 0ustar rootroot- parameter: spectra_path target: input_spectra/dummy_spectra.mgf - parameter: library_path target: input_library/ms2query_random_forest_model.onnx - parameter: library_path target: input_library/ms2ds_model_GNPS_15_12_2021.hdf5 - parameter: library_path target: input_library/ms2query_library.sqlite - parameter: library_path target: input_library/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy - parameter: library_path target: input_library/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt - parameter: library_path target: input_library/library_GNPS_15_12_2021_s2v_embeddings.pickle - parameter: library_path target: input_library/library_GNPS_15_12_2021_ms2ds_embeddings.pickle - parameter: library_path target: input_library/spec2vec_model_GNPS_15_12_2021.model - parameter: library_path target: input_library/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy input_library/0000755000000000000000000000000014540151521012435 5ustar rootrootinput_library/ms2query_library.sqlite0000777000000000000000000000000014540151521037265 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2query_library.sqliteustar rootrootinput_library/ms2query_random_forest_model.onnx0000777000000000000000000000000014540151521043363 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2query_random_forest_model.onnxustar rootroot././@LongLink0000644000000000000000000000015700000000000011605 Kustar rootroot/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npyinput_library/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy0000777000000000000000000000000014540151521045650 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.wv.vustar rootrootinput_library/spec2vec_model_GNPS_15_12_2021.model0000777000000000000000000000000014540151521042025 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.modelustar rootroot././@LongLink0000644000000000000000000000015400000000000011602 Kustar rootroot/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npyinput_library/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy0000777000000000000000000000000014540151521045106 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.syn1ustar rootroot././@LongLink0000644000000000000000000000015100000000000011577 Kustar rootroot/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_s2v_embeddings.pickleinput_library/library_GNPS_15_12_2021_s2v_embeddings.pickle0000777000000000000000000000000014540151521044756 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_s2v_embeddings.piustar rootroot././@LongLink0000644000000000000000000000017300000000000011603 Kustar rootroot/data/nf_data/useruploads/shared/ms2query/positiveim_model/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txtinput_library/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt0000777000000000000000000000000014540151521050755 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ALL_GNPS_210409_positive_processed_annotaustar rootrootinput_library/ms2ds_model_GNPS_15_12_2021.hdf50000777000000000000000000000000014540151521040135 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2ds_model_GNPS_15_12_2021.hdf5ustar rootroot././@LongLink0000644000000000000000000000015300000000000011601 Kustar rootroot/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_ms2ds_embeddings.pickleinput_library/library_GNPS_15_12_2021_ms2ds_embeddings.pickle0000777000000000000000000000000014540151521045261 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_ms2ds_embeddings.ustar rootrootinput_spectra/0000755000000000000000000000000014540151521012432 5ustar rootrootinput_spectra/dummy_spectra.mgf0000777000000000000000000000000014540151521031516 2/data/nf_data/useruploads/alberto/ms2query/dummy_spectra.mgfustar rootrootjob_dag.html0000644000000000000000000001217214540152246012035 0ustar rootroot Nextflow Cytoscape.js with Dagre

Nextflow Cytoscape.js with Dagre

job_parameters.yaml0000644000000000000000000000132714540151521013436 0ustar rootrootOMETAFLOW_SERVER: http://ometaflow-launchserver:4000 OMETALIBRARY_SERVER: http://ometalibrary-web:5000/library OMETAMASST_SERVER: http://ometamasst-web:5000/masst OMETATASK: 8979365f96f8468d98ad7ba919b4e4af OMETAUSER: alberto additional_metadata: retention_time feature_id create_time: 2023-12-18 15:17:27 PST-0800 description: '' ion_mode: positive library_path: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/input_library outdir: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af spectra_path: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/input_spectra task: 8979365f96f8468d98ad7ba919b4e4af workflow_version: SERVER:0.1.2;WORKFLOW:0.2 workflowname: ms2query_nextflow_workflow job_report.html0000644000000000000000001311551514540152245012625 0ustar rootroot [festering_lavoisier] Nextflow Workflow Report

Nextflow workflow report

[festering_lavoisier]

Workflow execution completed successfully!
Run times
18-Dec-2023 23:17:59 - 18-Dec-2023 23:23:01 (duration: 5m 2s)
  1 succeeded  
  0 cached  
  0 ignored  
  0 failed  
Nextflow command
nextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -with-weblog 'http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af' -c /app/launchserver/nextflow.config
CPU-Hours
0.1
Launch directory
/data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af
Work directory
/data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af
Project directory
/app/workflows_user/ms2query_nextflow_workflow
Script name
nf_workflow.nf
Script ID
05d0f9bfbd6d4117d83a84fa0ed552d1
Workflow session
5e855e67-600e-402d-b044-39d8f4b4cfa6
Workflow profile
standard
Nextflow version
version 21.10.0, build 5640 (11-11-2021 18:27 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)
job_timeline.html0000644000000000000000000075374114540152245013125 0ustar rootroot

Processes execution timeline

Launch time:
Elapsed time:
Legend: job wall time / memory usage (RAM)

nextflow_stdout.log0000644000000000000000000000121314540152247013530 0ustar rootrootN E X T F L O W ~ version 21.10.0 Launching `/app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf` [festering_lavoisier] - revision: 05d0f9bfbd [- ] process > processMS2query - [- ] process > processMS2query [ 0%] 0 of 1 executor > local (1) [b3/61469f] process > processMS2query [ 0%] 0 of 1 executor > local (1) [b3/61469f] process > processMS2query [ 0%] 0 of 1 ✔ executor > local (1) [b3/61469f] process > processMS2query [100%] 1 of 1 ✔ executor > local (1) [b3/61469f] process > processMS2query [100%] 1 of 1 ✔ Completed at: 18-Dec-2023 23:23:08 Duration : 5m 7s CPU hours : 0.1 Succeeded : 1 nf_cmd.sh0000644000000000000000000000116014540151521011332 0ustar rootrootnextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -with-weblog http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af -c /app/launchserver/nextflow.confignf_output/0000755000000000000000000000000014540152237011602 5ustar rootrootnf_output/results/0000755000000000000000000000000014540152237013303 5ustar rootrootnf_output/results/dummy_spectra.csv0000644000000000000000000000420214540152237016672 0ustar rootrootquery_spectrum_nr,ms2query_model_prediction,precursor_mz_difference,precursor_mz_query_spectrum,precursor_mz_analog,inchikey,analog_compound_name,smiles,retention_time,feature_id,cf_kingdom,cf_superclass,cf_class,cf_subclass,cf_direct_parent,npc_class_results,npc_superclass_results,npc_pathway_results 1,0.9323,0.0000,667.1150,667.1150,USXIYWCPCGVOKF,Hectochlorin,C[C@H]1[C@@H](OC(C2=CSC([C@H](C(C)(OC(C3=CSC([C@H](C(C)(O)C)OC1=O)=N3)=O)C)OC(C)=O)=N2)=O)CCCC([37Cl])(Cl)C,,,Organic compounds,Organic acids and derivatives,Peptidomimetics,Depsipeptides,Cyclic depsipeptides,Cyclic peptides; Depsipeptides,Oligopeptides,Amino acids and Peptides; Polyketides 2,0.9453,0.0000,553.1300,553.1300,DJXURFUTIYZESV,1-Caffeoyl-5-feruloylquinic acid,COC1=C(C=CC(=C1)/C=C/C(=O)O[C@@H]2C[C@](C[C@H]([C@@H]2O)O)(C(=O)O)OC(=O)/C=C/C3=CC(=C(C=C3)O)O)O,,,Organic compounds,Organic oxygen compounds,Organooxygen compounds,Alcohols and polyols,Quinic acids and derivatives,Cinnamic acids and derivatives,Phenylpropanoids (C6-C3),Shikimates and Phenylpropanoids 3,0.8810,0.0000,212.0820,212.0820,APVQOOKHDZVJEX,Mirapex,CCCN[C@H]1CCC2=C(C1)SC(=N2)N.O.Cl.Cl,,,Organic compounds,Organic nitrogen compounds,Organonitrogen compounds,Amines,Aralkylamines,,,Alkaloids 4,0.9453,0.0000,850.6360,850.6360,VCAGNEUDNVLWPT,Halovir C,CCCCCCCCCCCCCC(=O)NC(C)(C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)NC(CCC(N)=O)C(=O)N[C@H](CO)CC(C)C,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,"Amino acids, peptides, and analogues",Oligopeptides,Linear peptides; Lipopeptides,Oligopeptides,Amino acids and Peptides 5,0.8820,0.0000,431.2080,431.2080,QFKOZHNKLSMVDN,,C[C@H](N1C(=O)N2CCc3c([nH]c4ccccc34)[C@@]2(C)C1=O)C(=O)NCc5ccc(C)cc5,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,"Amino acids, peptides, and analogues",Dipeptides,Carboline alkaloids,Tryptophan alkaloids,Alkaloids 6,0.8763,0.0000,236.0110,236.0110,PZXOQEXFMJCDPG,Pesticide1_Omethoate_C5H12NO4PS_,CNC(=O)CSP(=O)(OC)OC,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,Carboxylic acid derivatives,Secondary carboxylic acid amides,,, nf_output/ms2query_results.zip0000644000000000000000000000234614540152237015703 0ustar rootrootPK Wresults/UT ӀeӀeux PKW#yresults/dummy_spectra.csvUT ԀeӀeux Umo8ί@H.KB92mپ$Ѳl*:.X8v$']N:U<33ste).HjdsE&*f"J59͹ -tti&)6IZ!.oXj;*IU!H,eHIsls` "#m\*10+R Yfd>"R#:,,+DU6{tJR?\DžiF}Zn+" ~ Ǽ H]+ JVQFlunε*oV?>TIAo s \3YT3=<:OFs=m_ cN MKt5IO) 1Pj%y{j0drJ)-2nk h #w |rM` ]l. U~ۋV B\w1&T %$~UtSTݷ`هB1nUO?,WӤе`7g̿_/>vǞU gtHp1jٍzRpjfK*v.ѭ.\k"[k\ǣ&]wv tyv}9t 4gG4쵂7?aC3 B=ߜQ%c.= PK WAresults/UTӀeux PKW#yBresults/dummy_spectra.csvUTԀeux PK#nf_resume_cmd.sh0000644000000000000000000000117014540151521012713 0ustar rootrootnextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -resume -with-weblog http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af -c /app/launchserver/nextflow.configsubmission_parameters.yaml0000644000000000000000000000055614540151521015062 0ustar rootrootadditional_metadata: retention_time feature_id create_time: 2023-12-18 15:17:27 PST-0800 description: '' ion_mode: positive library_path: USERUPLOAD/shared/ms2query/positiveim_model spectra_path: USERUPLOAD/alberto/ms2query/dummy_spectra.mgf task: 8979365f96f8468d98ad7ba919b4e4af workflow_version: SERVER:0.1.2;WORKFLOW:0.2 workflowname: ms2query_nextflow_workflow workflowdisplay.yaml0000644000000000000000000000037314540151521013701 0ustar rootrootname: ms2query_nextflow_workflow displayname: results Views: - name: MS2Query results zip displayname: MS2Query results zip viewname: ms2query_zip_file displaytype: download parameters: filename: nf_output/ms2query_results.zip