IGVF-1977-peak-quantification

src/igvfd/schemas/changelogs/analysis_step.md

@@ -2,6 +2,8 @@
 
 ### Minor changes since schema version 5
 
+* Extend `input_content_types` enum list to include `peak quantifications`.
+* Extend `output_content_types` enum list to include `peak quantifications`.
 * Extend `input_content_types` enum list to include `variant localization impacts`.
 * Extend `output_content_types` enum list to include `variant localization impacts`.
 * Extend `input_content_types` enum list to include `external source data`.

src/igvfd/schemas/changelogs/tabular_file.md

@@ -2,6 +2,7 @@
 
 ### Minor changes since schema version 12
 
+* Extend `content_type` enum list to include `peak quantifications`.
 * Extend `content_type` enum list to include `variant localization impacts`.
 
 ### Schema version 12

src/igvfd/schemas/tabular_file.json

@@ -129,6 +129,7 @@
  "loci",
  "MPRA sequence designs",
  "peaks",
+ "peak quantifications",
  "prime editing guide RNA sequences",
  "protein to protein interaction score",
  "sample sort parameters",
@@ -161,6 +162,7 @@
  "external source data": "File containing a list of urls used as a source.",
  "MPRA sequence designs": "Sequences designed for an MPRA experiment. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/table_schemas/mpra_sequence_designs.json.",
  "peaks": "Detected genomic regions of relative enrichment in coverage data, such as peaks in ChIP-seq or ATAC-seq indicating protein binding sites or chromatin accessibility.",
+ "peak quantifications": "The quantified levels of peaks detected in ChIP-seq or ATAC-seq assays.",
  "prime editing guide RNA sequences": "The sequences of guide RNAs designed for prime editing CRISPR experiments. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/table_schemas/prime_editing_guide_rna_sequences.json.",
  "protein to protein interaction score": "Scores or metrics for interactions between proteins.",
  "sample sort parameters": "The parameters/quantifications used for sorting biological samples, such as those in flow cytometry.",

src/igvfd/tests/data/inserts/tabular_file.json

@@ -259,5 +259,24 @@
  "assembly": "GRCh38",
  "file_set": "IGVFDS3333DDDD",
  "controlled_access": false
+ },
+ {
+ "uuid": "f47ac10b-58cc-4372-a567-0e02b2c3d479",
+ "lab": "j-michael-cherry",
+ "award": "HG012012",
+ "aliases": [
+ "igvf:peak_quantifications"
+ ],
+ "status": "released",
+ "release_timestamp": "2024-06-09T12:34:56Z",
+ "md5sum": "17d63c7c831bbcf0637516cc15e694c4",
+ "file_format": "tsv",
+ "content_type": "peak quantifications",
+ "submitted_file_name": "/Users/igvf/igvf_files/peak_quantifications.tsv.gz",
+ "file_size": 3139,
+ "upload_status": "validated",
+ "assembly": "GRCh38",
+ "file_set": "IGVFDS3333DDDD",
+ "controlled_access": false
  }
 ]