Updated Germline workflow run

02-Cromwell-Azure/README.md

@@ -57,13 +57,12 @@ Here is an example of running the germline alignment and variant calling pipelin
 - Navigate to the germline Github with the above link
 - Download `WholeGenomeGermlineSingleSample.trigger.json` trigger json file
 - Start your workflow
-    - Navigate to the default storage account. 
-    - In the `workflows` container, place the trigger JSON file `WholeGenomeGermlineSingleSample.trigger.json` in the `new` directory via Azure Portal or Azure Storage Explorer. This initiates a Cromwell workflow. **NOTE** In the trigger JSON file, `WorkflowUrl` points to the WDL file `WholeGenomeGermlineSingleSample.wdl` and `WorkflowinputsUrl` points to input file `WholeGenomeGermlineSingleSample.inputs.json`, both are in the same Github. These files could be added as-is or updated for your functionality to `inputs` container and trigger file pointing to the `input` container.
-    - Break-down of the WDL file `WholeGenomeGermlineSingleSample.wdl`
-        - This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practicesfor germline SNP and Indel discovery in human whole-genome data using 6 WDL files from the same Github: UnmappedBamToAlignedBam.wdl, AggregatedBamQC.wdl, Qc.wdl, BamToCram.wdl, VariantCalling.wdl, GermlineStructs.wdl. Within each of these WDL files, and many sub WDL files.
+    - Navigate to the default storage account created above. 
+    - In the `workflows` container, place the trigger json file `WholeGenomeGermlineSingleSample.trigger.json` in the `new` directory via Azure Portal or Azure Storage Explorer. This initiates a Cromwell workflow. In the trigger jsonfile, `WorkflowUrl` points to the WDL file `WholeGenomeGermlineSingleSample.wdl` and `WorkflowinputsUrl` points to input file `WholeGenomeGermlineSingleSample.inputs.json`, both are in the same [Github](https://github.com/microsoft/gatk4-genome-processing-pipeline-azure#germline-alignment-and-variant-calling-pipeline-on-azure). These files could be added as-is or updated for your functionality to `inputs` container and trigger file updated to point to the `input` container.
+    - Break-down of the WDL file `WholeGenomeGermlineSingleSample.wdl`. This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human whole-genome data using 6 WDL files from the same Github: `UnmappedBamToAlignedBam.wdl, AggregatedBamQC.wdl, Qc.wdl, BamToCram.wdl, VariantCalling.wdl, GermlineStructs.wdl`. Within each of these WDL files are many sub WDL files.
     - The workflow returns a workflow ID that is appended to the trigger JSON file name and transferred to the `inprogress` directory in the workflows container. 
     - Once your workflow completes, you can view the output files of your workflow in the `cromwell-executions` container. 6 folders are created for the 6 import WDL files, and sub-folders within each for the sub-import WDL files and so on.
-    - Additional output files from the Cromwell endpoint, including metadata and the timing file, are found in the `outputs` container. **NOTE** The outputs.json file shows all outputs created and where they are stored. To learn more about Cromwell's metadata and timing information, visit the Cromwell documentation.
+    - Additional output files from the Cromwell endpoint, including metadata and the timing file, are found in the `outputs` container. The outputs.json file shows all outputs created and where they are stored. To learn more about Cromwell's metadata and timing information, visit the [Cromwell documentation](https://cromwell.readthedocs.io/en/stable/).
     - To abort a workflow that is in-progress, navigate to `workflows` container, place an empty file in the "abort" virtual directory named cromwellID.json, where "cromwellID" is the Cromwell workflow ID you wish to abort.
     - [More details](https://github.com/microsoft/CromwellOnAzure/blob/master/docs/managing-your-workflow.md/#start-your-workflow)