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@@ -57,3 +57,251 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
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lcms/fbmn.mgf

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d0666a7abe0691e5d0bd7560476ebde85b3eadcd41ccc6eac8e360f890ac949f
+size 31120887

lcms/fbmn/gnps2/flow_filelinking.yaml

@@ -0,0 +1,114 @@
+- parameter: inputfeatures
+  target: inputfeatures/fbmn_quant.csv
+- parameter: inputspectra
+  target: inputspectra/fbmn.mgf
+- parameter: metadata_filename
+  target: metadata_filename/fbmn_metadata.tsv
+- parameter: input_libraries
+  target: input_libraries/MMV_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-PESTICIDES-POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/BMDMS-NP.mgf
+- parameter: input_libraries
+  target: input_libraries/LEAFBOT.mgf
+- parameter: input_libraries
+  target: input_libraries/BIRMINGHAM-UHPLC-MS-NEG.mgf
+- parameter: input_libraries
+  target: input_libraries/DEREPLICATOR_IDENTIFIED_LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/RESPECT.mgf
+- parameter: input_libraries
+  target: input_libraries/MIADB.mgf
+- parameter: input_libraries
+  target: input_libraries/NEO-MSMS.mgf
+- parameter: input_libraries
+  target: input_libraries/HCE-CELL-LYSATE-LIPIDS.mgf
+- parameter: input_libraries
+  target: input_libraries/CASMI.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/PSU-MSMLS.mgf
+- parameter: input_libraries
+  target: input_libraries/IQAMDB.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SELLECKCHEM-FDA-PART1.mgf
+- parameter: input_libraries
+  target: input_libraries/XANTHONES-DB.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-D2-AMINO-LIPID-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/HMDB.mgf
+- parameter: input_libraries
+  target: input_libraries/BIRMINGHAM-UHPLC-MS-POS.mgf
+- parameter: input_libraries
+  target: input_libraries/MMV_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/DRUGS-OF-ABUSE-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/MASSBANK.mgf
+- parameter: input_libraries
+  target: input_libraries/BILELIB19.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-IOBA-NHC.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-MSMLS.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-EMBL-MCF.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-CLINICALCOLLECTION2.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/MONA.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NUTRI-METAB-FEM-POS.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SAM-SIK-KANG-LEGACY-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/PNNL-LIPIDS-POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-CLINICALCOLLECTION1.mgf
+- parameter: input_libraries
+  target: input_libraries/UM-NPDC.mgf
+- parameter: input_libraries
+  target: input_libraries/LDB_POSITIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/MASSBANKEU.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SELLECKCHEM-FDA-PART2.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-COLLECTIONS-MISC.mgf
+- parameter: input_libraries
+  target: input_libraries/ECG-ACYL-ESTERS-C4-C24-LIBRARY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIST14-MATCHES.mgf
+- parameter: input_libraries
+  target: input_libraries/PNNL-LIPIDS-NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-FAULKNERLEGACY.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-PRESTWICKPHYTOCHEM.mgf
+- parameter: input_libraries
+  target: input_libraries/BERKELEY-LAB.mgf
+- parameter: input_libraries
+  target: input_libraries/SUMNER.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/LDB_NEGATIVE.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-NUTRI-METAB-FEM-NEG.mgf
+- parameter: input_libraries
+  target: input_libraries/TUEBINGEN-NATURAL-PRODUCT-COLLECTION.mgf
+- parameter: input_libraries
+  target: input_libraries/GNPS-SCIEX-LIBRARY.mgf

lcms/fbmn/gnps2/job_dag.html

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+<!--
+  ~ Copyright 2013-2019, Centre for Genomic Regulation (CRG)
+  ~
+  ~ Licensed under the Apache License, Version 2.0 (the "License");
+  ~ you may not use this file except in compliance with the License.
+  ~ You may obtain a copy of the License at
+  ~
+  ~     http://www.apache.org/licenses/LICENSE-2.0
+  ~
+  ~ Unless required by applicable law or agreed to in writing, software
+  ~ distributed under the License is distributed on an "AS IS" BASIS,
+  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  ~ See the License for the specific language governing permissions and
+  ~ limitations under the License.
+  -->
+
+<html>
+
+    <head>
+        <title>Nextflow Cytoscape.js with Dagre</title>
+
+        <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
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+        <script>
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+    </body>
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+</html>

lcms/fbmn/gnps2/job_parameters.yaml

@@ -0,0 +1,31 @@
+OMETAFLOW_SERVER: http://ometaflow-launchserver:4000
+OMETALIBRARY_SERVER: http://ometalibrary-web:5000/library
+OMETAMASST_SERVER: http://ometamasst-web:5000/masst
+OMETATASK: a844d8ee4f534c21950b031d70b7254f
+OMETAUSER: Tito_Damiani
+create_time: 2024-03-16 20:46:20 PDT-0700
+description: 20240316_piperNET_FBMN
+featurefindingtool: MZMINE
+fragment_tolerance: '0.01'
+input_libraries: /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/input_libraries
+input_raw_spectra: NO_FILE
+input_supplemental_edges: NO_FILE
+inputfeatures: /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/inputfeatures/fbmn_quant.csv
+inputspectra: /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/inputspectra
+library_analog_search: '1'
+library_min_cosine: '0.7'
+library_min_matched_peaks: '6'
+library_topk: '1'
+metadata_filename: /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/metadata_filename/fbmn_metadata.tsv
+min_peak_intensity: '0.0'
+networking_max_shift: '1999'
+networking_min_cosine: '0.7'
+networking_min_matched_peaks: '6'
+normalization: None
+pm_tolerance: '0.01'
+precursor_filter: 'yes'
+publishdir: /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f
+task: a844d8ee4f534c21950b031d70b7254f
+window_filter: 'yes'
+workflow_version: SERVER:0.1.2;WORKFLOW:0.5.8
+workflowname: feature_based_molecular_networking_workflow

lcms/fbmn/gnps2/nf_cmd.sh

@@ -0,0 +1 @@
+nextflow run /app/workflows_user/feature_based_molecular_networking_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/job_parameters.yaml -w /data/nf_data/server/nf_work/a844d8ee4f534c21950b031d70b7254f -with-report /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/job_report.html -with-timeline /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/a844d8ee4f534c21950b031d70b7254f/job_dag.html -with-weblog http://localhost:4000/nf_weblog/a844d8ee4f534c21950b031d70b7254f -c /app/launchserver/nextflow.config

lcms/fbmn/gnps2/nf_output/clustering/specs_ms.mgf

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lcms/fbmn/gnps2/nf_output/clustering/spectra_filtered.mgf

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lcms/fbmn/gnps2/nf_output/clustering/spectra_reformatted.mgf

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lcms/fbmn/gnps2/nf_output/filesummary/summaryresult.tsv

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+

lcms/fbmn/gnps2/nf_output/metadata/merged_metadata.tsv

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lcms/fbmn/gnps2/nf_output/networking/clustersummary_with_groups.tsv

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lcms/fbmn/gnps2/nf_output/networking/clustersummary_with_network.tsv

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lcms/fbmn/gnps2/nf_output/networking/network.graphml

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lcms/fbmn/gnps2/nf_output/networking/network_singletons.graphml

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lcms/fbmn/gnps2/nf_output/networking/params/0.params

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lcms/fbmn/gnps2/nf_output/networking/params/1.params

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lcms/fbmn/gnps2/nf_output/networking/params/10.params

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lcms/fbmn/gnps2/nf_output/networking/params/11.params

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lcms/fbmn/gnps2/nf_output/networking/params/12.params

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+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=12108
+IDX_END=13116

lcms/fbmn/gnps2/nf_output/networking/params/13.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=13117
+IDX_END=14138

lcms/fbmn/gnps2/nf_output/networking/params/2.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=2018
+IDX_END=3026

lcms/fbmn/gnps2/nf_output/networking/params/3.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=3027
+IDX_END=4035

lcms/fbmn/gnps2/nf_output/networking/params/4.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=4036
+IDX_END=5044

lcms/fbmn/gnps2/nf_output/networking/params/5.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=5045
+IDX_END=6053

lcms/fbmn/gnps2/nf_output/networking/params/6.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=6054
+IDX_END=7062

lcms/fbmn/gnps2/nf_output/networking/params/7.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=7063
+IDX_END=8071

lcms/fbmn/gnps2/nf_output/networking/params/8.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=8072
+IDX_END=9080

lcms/fbmn/gnps2/nf_output/networking/params/9.params

@@ -0,0 +1,9 @@
+ALIGNS_FORMAT=tsv
+MIN_MATCHED_PEAKS=6
+TOLERANCE_PEAK=0.01
+TOLERANCE_PM=0.01
+PAIRS_MIN_COSINE=0.7
+MAX_SHIFT=1999.0
+INPUT_SPECTRA_MS2=spectra_filtered.mgf
+IDX_START=9081
+IDX_END=10089