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PiperNET

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4

Rename raw/lcms/datafiles to rawfiles; move external/gnps2 to external/molecular_networks/gnps2

#4
by titodamiani - opened
base: refs/heads/main
←
from: refs/pr/4
Discussion Files changed
+151
-2
This view is limited to 50 files because it contains too many changes. See the raw diff here.
Files changed (50) hide show
  1. .gitattributes +148 -0
  2. README.md +3 -2
  3. external/{gnps2 → molecular_networks/gnps2}/fbmn/flow_filelinking.yaml +0 -0
  4. external/{gnps2 → molecular_networks/gnps2}/fbmn/job_dag.html +0 -0
  5. external/{gnps2 → molecular_networks/gnps2}/fbmn/job_parameters.yaml +0 -0
  6. external/{gnps2 → molecular_networks/gnps2}/fbmn/job_report.html +0 -0
  7. external/{gnps2 → molecular_networks/gnps2}/fbmn/job_timeline.html +0 -0
  8. external/{gnps2 → molecular_networks/gnps2}/fbmn/nextflow_stdout.log +0 -0
  9. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_cmd.sh +0 -0
  10. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/3-HYDROXY-ACYL-AMIDES-LIBRARY.mgf.tsv +0 -0
  11. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/AASDB.mgf.tsv +0 -0
  12. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/BERKELEY-LAB.mgf.tsv +0 -0
  13. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/BILELIB19.mgf.tsv +0 -0
  14. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/BIRMINGHAM-UHPLC-MS-NEG.mgf.tsv +0 -0
  15. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/BIRMINGHAM-UHPLC-MS-POS.mgf.tsv +0 -0
  16. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/BMDMS-NP.mgf.tsv +0 -0
  17. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/CASMI.mgf.tsv +0 -0
  18. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/CMMC-FOOD-BIOMARKERS.mgf.tsv +0 -0
  19. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/DEREPLICATOR_IDENTIFIED_LIBRARY.mgf.tsv +0 -0
  20. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/DMIM-DRUG-METABOLITE-LIBRARY.mgf.tsv +0 -0
  21. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/DRUGS-OF-ABUSE-LIBRARY.mgf.tsv +0 -0
  22. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/ECG-ACYL-AMIDES-C4-C24-LIBRARY.mgf.tsv +0 -0
  23. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/ECG-ACYL-ESTERS-C4-C24-LIBRARY.mgf.tsv +0 -0
  24. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/ECRFS_DB.mgf.tsv +0 -0
  25. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/ELIXDB-LICHEN-DATABASE.mgf.tsv +0 -0
  26. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-COLLECTIONS-MISC.mgf.tsv +0 -0
  27. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE.mgf.tsv +0 -0
  28. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-COLLECTIONS-PESTICIDES-POSITIVE.mgf.tsv +0 -0
  29. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-D2-AMINO-LIPID-LIBRARY.mgf.tsv +0 -0
  30. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-EMBL-MCF.mgf.tsv +0 -0
  31. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-FAULKNERLEGACY.mgf.tsv +0 -0
  32. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-IOBA-NHC.mgf.tsv +0 -0
  33. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-LIBRARY.mgf.tsv +0 -0
  34. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-MSMLS.mgf.tsv +0 -0
  35. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-N-ACYL-LIPIDS-MASSQL.mgf.tsv +0 -0
  36. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-CLINICALCOLLECTION1.mgf.tsv +0 -0
  37. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-CLINICALCOLLECTION2.mgf.tsv +0 -0
  38. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY.mgf.tsv +0 -0
  39. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE.mgf.tsv +0 -0
  40. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_POSITIVE.mgf.tsv +0 -0
  41. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE.mgf.tsv +0 -0
  42. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NIST14-MATCHES.mgf.tsv +0 -0
  43. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NUTRI-METAB-FEM-NEG.mgf.tsv +0 -0
  44. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-NUTRI-METAB-FEM-POS.mgf.tsv +0 -0
  45. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-PRESTWICKPHYTOCHEM.mgf.tsv +0 -0
  46. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-SAM-SIK-KANG-LEGACY-LIBRARY.mgf.tsv +0 -0
  47. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-SCIEX-LIBRARY.mgf.tsv +0 -0
  48. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-SELLECKCHEM-FDA-PART1.mgf.tsv +0 -0
  49. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/GNPS-SELLECKCHEM-FDA-PART2.mgf.tsv +0 -0
  50. external/{gnps2 → molecular_networks/gnps2}/fbmn/nf_output/HCE-CELL-LYSATE-LIPIDS.mgf.tsv +0 -0
.gitattributes CHANGED
@@ -419,3 +419,151 @@ raw/rnaseq/piper56/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text
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  raw/rnaseq/piper56/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text
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  raw/rnaseq/piper56/transcriptome.pep filter=lfs diff=lfs merge=lfs -text
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  raw/rnaseq/piper56/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  raw/rnaseq/piper56/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text
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  raw/rnaseq/piper56/transcriptome.pep filter=lfs diff=lfs merge=lfs -text
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  raw/rnaseq/piper56/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/clustering/specs_ms.mgf filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/clustering/spectra_reformatted.mgf filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/clustering/tall_raw_data.tsv filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/networking/clustersummary_with_groups.tsv filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/networking/clustersummary_with_network.tsv filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/networking/network.graphml filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn/nf_output/networking/network_singletons.graphml filter=lfs diff=lfs merge=lfs -text
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+ external/molecular_networks/gnps2/fbmn_global.cys filter=lfs diff=lfs merge=lfs -text
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+ raw/lcms/rawfiles/202312_04_BlankExtr-1_1uL.mzML filter=lfs diff=lfs merge=lfs -text
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+ raw/lcms/rawfiles/202312_05_BlankExtr-2_1uL.mzML filter=lfs diff=lfs merge=lfs -text
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+ raw/lcms/rawfiles/202312_08_P06-Leaf-r1_1uL.mzML filter=lfs diff=lfs merge=lfs -text
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+ raw/lcms/rawfiles/202312_122_P32-Leaf-r1_1uL.mzML filter=lfs diff=lfs merge=lfs -text
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README.md CHANGED
@@ -22,7 +22,7 @@ data/
22
  ├── README.md # this dataset card
23
  ├── raw/
24
  │ ├── lcms/
25
- │ │ ├── datafiles/ # LC-MS raw files, mzML (140 files)
26
  │ │ └── metadata.tsv # sample metadata, read by MZmine
27
  │ └── rnaseq/piperNN/ # transXpress output, one folder per sample ID (13)
28
  │ ├── transcriptome.fasta # de novo assembly
@@ -34,7 +34,8 @@ data/
34
  │ ├── lcms_mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml)
35
  │ └── rnaseq_clstr/piperNN/ # CD-HIT clustered proteomes
36
  ├── external/
37
- │ ├── gnps2/ # GNPS2 feature-based molecular networking results
 
38
  │ ├── sirius/ # SIRIUS results: CSI:FingerID structures, CANOPUS classes
39
  │ ├── orthogroups/sonicpd/ # SonicParanoid orthogroups
40
  │ ├── speclibs/ # MS/MS spectral libraries for annotation in MZmine
 
22
  ├── README.md # this dataset card
23
  ├── raw/
24
  │ ├── lcms/
25
+ │ │ ├── rawfiles/ # LC-MS raw files, mzML (140 files)
26
  │ │ └── metadata.tsv # sample metadata, read by MZmine
27
  │ └── rnaseq/piperNN/ # transXpress output, one folder per sample ID (13)
28
  │ ├── transcriptome.fasta # de novo assembly
 
34
  │ ├── lcms_mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml)
35
  │ └── rnaseq_clstr/piperNN/ # CD-HIT clustered proteomes
36
  ├── external/
37
+ │ ├── molecular_networks/
38
+ │ │ └── gnps2/ # GNPS2 feature-based molecular networking results
39
  │ ├── sirius/ # SIRIUS results: CSI:FingerID structures, CANOPUS classes
40
  │ ├── orthogroups/sonicpd/ # SonicParanoid orthogroups
41
  │ ├── speclibs/ # MS/MS spectral libraries for annotation in MZmine
external/{gnps2 → molecular_networks/gnps2}/fbmn/flow_filelinking.yaml RENAMED
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