Juranic/histology dirschema update (#1314)

* Update histology-v2.yaml

Add qptiff to /raw/images/

* Update CHANGELOG.md

Update Histology directory schema

* Docs: Update histology docs

---------

Co-authored-by: Juan Puerto <=>

CHANGELOG.md

@@ -21,6 +21,7 @@
 - Update Histology with links
 - Update GeoMx NGS directory schema
 - Ported murine from SenNet
+- Update Histology directory schema
 
 ## v0.0.17
 

docs/histology/current/index.md

@@ -37,7 +37,7 @@ Related files:
 | <code>extras\/microscope_settings\.json</code> |  | **[QA/QC]** A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <[email protected]> if help is required in generating this document. |  |
 | <code>raw\/.*</code> | ✓ | Raw data files for the experiment. |  |
 | <code>raw\/images\/.*</code> | ✓ | Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file. |  |
-| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff)</code> | ✓ | Raw microscope file for the experiment |  |
+| <code>raw\/images\/[^\/]+\.(?:xml&#124;scn&#124;vsi&#124;ndpi&#124;svs&#124;czi&#124;tiff&#124;qptiff)</code> | ✓ | Raw microscope file for the experiment |  |
 | <code>lab_processed\/.*</code> | ✓ | Experiment files that were processed by the lab generating the data. |  |
 | <code>lab_processed\/images\/.*</code> | ✓ | Processed image files |  |
 | <code>lab_processed\/images\/[^\/]+\.ome\.tiff</code> (example: <code>lab_processed/images/HBM892.MDXS.293.ome.tiff</code>) | ✓ | OME-TIFF files (multichannel, multi-layered) produced by the microscopy experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. <https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0> |  |

src/ingest_validation_tools/directory-schemas/histology-v2.yaml

@@ -22,7 +22,7 @@ files:
     required: True
     description: Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file.
   -
-    pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff)
+    pattern: raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff)
     required: True
     description: Raw microscope file for the experiment
     is_qa_qc: False