Juranic/lcms dirschema updates (#1363)

* Create lcms-v2.2.yaml

Changed lab_processed/ , lab_processed/ID_search_results/  and lab_processed/ID_metadata/  directories to optional.

* Update CHANGELOG.md

* Documentation: Update LCMS docs

---------

Co-authored-by: Juan Puerto <=>

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## v0.0.26 (in progress)
 - Update GeoMx NGS directory schema
 - Update MERFISH directory schema
+- Update LC-MS directory schema
 
 ## v0.0.25
 - Update GeoMx NGS directory schema

docs/lcms/current/index.md

@@ -28,7 +28,24 @@ Related files:
 <br>
 
 ## Directory schemas
-<summary><b>Version 2.0 (use this one)</b></summary>
+<summary><b>Version 2.2 (use this one)</b></summary>
+
+| pattern | required? | description |
+| --- | --- | --- |
+| <code>extras\/.*</code> | ✓ | Folder for general lab-specific files related to the dataset. |
+| <code>extras\/mass-spec_environment\.(?:json&#124;tsv)</code> |  | JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that's used to describe the imaging equipment. |
+| <code>raw\/.*</code> | ✓ | Raw data files for the experiment. |
+| <code>raw\/[^\/]+\.raw</code> (example: <code>raw/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw</code>) | ✓ | Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans. |
+| <code>raw\/[^\/]+\.(?:mzML&#124;d)</code> | ✓ | Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans. |
+| <code>lab_processed\/.*</code> |  | Lab processed files |
+| <code>lab_processed\/ID_search_results\/.*</code> |  | Identification results. |
+| <code>lab_processed\/ID_search_results\/[^\/]+\.csv</code> |  | Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data. In the case of MS1 this file should include a list of features. |
+| <code>lab_processed\/ID_metadata\/.*</code> |  | Identification search parameters/metadata. |
+| <code>lab_processed\/ID_metadata\/[^\/]+\.csv</code> |  | Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer). |
+| <code>lab_processed\/QC_results\/.*</code> |  | Output file resulting from QC analysis. |
+| <code>lab_processed\/QC_results\/[^\/]+\.txt</code> |  | A list of metrics with the score of the current dataset that shows the quality of data collection. |
+
+<summary><b>Version 2.0</b></summary>
 
 | pattern | required? | description |
 | --- | --- | --- |

src/ingest_validation_tools/directory-schemas/lcms-v2.2.yaml

@@ -0,0 +1,50 @@
+files:
+  -
+    pattern: extras\/.*
+    required: True
+    description: Folder for general lab-specific files related to the dataset.
+  -
+    pattern: extras\/mass-spec_environment\.(?:json|tsv)
+    required: False
+    description: JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that's used to describe the imaging equipment.
+  -
+    pattern: raw\/.*
+    required: True
+    description: Raw data files for the experiment.
+  -  
+    pattern: raw\/[^\/]+\.raw
+    required: True
+    description: Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans.
+    example: raw/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw
+  -  
+    pattern: raw\/[^\/]+\.(?:mzML|d)
+    required: True
+    description: Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans.
+  -
+    pattern: lab_processed\/.*
+    required: False
+    description: Lab processed files
+  -
+    pattern: lab_processed\/ID_search_results\/.*
+    required: False
+    description: Identification results. 
+  -
+    pattern: lab_processed\/ID_search_results\/[^\/]+\.csv
+    required: False
+    description: Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data. In the case of MS1 this file should include a list of features.
+  -
+    pattern: lab_processed\/ID_metadata\/.*
+    required: False
+    description: Identification search parameters/metadata.
+  -
+    pattern: lab_processed\/ID_metadata\/[^\/]+\.csv
+    required: False
+    description: Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer).
+  -
+    pattern: lab_processed\/QC_results\/.*
+    required: False
+    description: Output file resulting from QC analysis.
+  -
+    pattern: lab_processed\/QC_results\/[^\/]+\.txt
+    required: False
+    description: A list of metrics with the score of the current dataset that shows the quality of data collection.