fix: CQDG-00 add readme file

README.md

@@ -0,0 +1,74 @@
+<p align="center">
+  <img src="docs/cqdg_logo.svg" alt="CQDG repository logo" width="660px" />
+</p>
+
+## ETL (Clinical && Genomic)
+
+ETL that extracts clinical and genomic data for the CQDG data portal.
+
+## Run the ETL via StepFunctions
+
+The Clinical and Genomic ETLs can now be started via DAGs in Airflow. When the ETL finishes a status will be reported 
+to `cqdg-airflow` channel. Each step can be run separately for both clinical data or genomic data.
+
+### Clinical ETL
+* DAG ***etl*** (Runs all steps for clinical ETL: etl-fhir-import => etl-import => etl-prepare-index => etl-index => etl-publish)
+* DAG ***etl-fhir-import*** (Runs step fhavro-export for clinical ETL)
+* DAG ***etl-import*** (Runs step index-task for clinical ETL)
+* DAG ***etl-prepare-index*** (Runs step prepare-index for clinical ETL)
+* DAG ***etl-index*** (Runs step index-task for clinical ETL)
+* DAG ***etl-publish*** (Runs step publish-task for clinical ETL)
+
+Example Input JSON for ***etl*** DAG:
+```json
+{
+  "es_port":"9200",
+  "project":"cqdg",
+  "release_id":"14",
+  "study_codes":"study1,study2,study3,T-DEE"
+}
+```
+* release_id (required) - Release ID passed to Spark Jobs
+* study_codes (required)  - List of Study code to run Portal ETL against
+* es_port (required) - Port of Elasticsearch cluster, should be 9200
+* project - project, should be cqdg
+
+
+### Genomic ETL 
+* DAG ***etl-variant*** (Runs all steps for clinical ETL: enrich-specimen => etl-normalize-variants => 	etl-enrich-variants => etl-prepare-index-variant =>  etl-index)
+* DAG ***enrich-specimen*** (Runs step enrich-specimen for genomic ETL, enriching the current specimen tables)
+* DAG ***etl-normalize-variants*** (Runs step normalize for snv and for consequences)
+* DAG ***etl-enrich-variants*** (Runs step enrich for variants and for consequences)
+* DAG ***etl-prepare-index-variant*** (Runs step prepare index for variant_centric, gene_centric, variant_suggestions, gene_suggestions)
+* DAG ***etl-index*** (Runs step index-task for genomic ETL)
+* DAG ***etl-publish-variant*** (Runs step publish variant_centric, gene_centric, variant_suggestions, gene_suggestions)
+
+```json
+{
+  "study_code": "XYZ",
+  "owner": "person1",
+  "dateset_batches": [
+    {
+      "batches": [
+        "annotated_vcf1",
+        "annotated_vcf2"
+      ],
+      "dataset": "dataset_dataset1"
+    },
+    {
+      "batches": [
+        "annotated_vcf"
+      ],
+      "dataset": "dataset_dataset2"
+    }
+  ],
+  "release_id": 1,
+  "project": "cqdg",
+  "es_port": 9200
+}
+```
+* release_id (required) - Release ID passed to Spark Jobs
+* study_code (required)  - study_code
+* dateset_batches (required) - Batches to run
+* es_port (required) - Port of Elasticsearch cluster, should be 9200
+* project - project, should be cqdg