unknown
male
female
unspecified
other
ambiguous
not\_applicable
| false | | race | | Select |american\_indian\_or\_alaska\_native
asian
black\_or\_african\_american
native\_hawaiian\_or\_other\_pacific\_islander
not\_reported
unknown
white
| false | | ethnicity | | Select |hispanic\_or\_latino
not\_hispanic\_or\_latino
not\_reported
unknown
| false | | externalSpecimenId | | Text | | false | | hl7SpecimenId | | Text | | false | | studyIdentifier | | Text | | false | | studySubjectIdentifier | | Text | | false | | type | Sample Type | ForeignKey | MS | true | | panelName | | Text | | false | | sampleType | | Select | patientcare | true | | indication | | Text | | false | | identified | | Boolean | 1 | false | | disease | | ForeignKey | DS | false | | physicians | | ForeignKeys | PA | false | | accessionNumber | | Text | | false | | case | | CGWCase | | false | | lane | | Number | 1 | false | | barcode | | Text | | false | | runType | This identifies whether the sequencing was done using paired end or single end. | Select | pairedEnd | false | | analysis\_related\_files | | CGWUploadFile | | false | **Patients:** No specific columns are required. However, the name field have to be: `[First Name] [Last Name]` **Disease:** | Name | Widget | Default value | Is required | | ------------ | ------ | ------------- | ----------- | | code | Number | | TRUE | | code\_system | Text | SNOMED-CT | TRUE | **Mass:** | Name | Widget | Default value | Is required | | ------------ | ------ | ------------- | ----------- | | code | Number | | TRUE | | code\_system | Text | SNOMED-CT | TRUE | ### Default Sections Add a default section so that all new records will have the same section. The default section is only needed for samples: * **Job**, use the widget of **CGWJob** ### Import data If you already have some data for samples, patients, disease, and/or mass, use [Import](/user-guide/list-view.md#import) function to import them first. ## CGWCase CGWCase is a widget to create or update a Case. ### Create a case Click the *edit* icon and the widget shall collect all necessary information to create a case. Error message will be provided if certain data is missing. Click **Create Case** button to create a case. If successful, a case id will be stored for the column. ### Update a case The detail of a case can be updated via update a case. To do that, click the *edit* icon, and then click the **Update Case** button. ### Clear case data If for some reason, you want to discard the case and redo the analysis. You can click **Clear Case** button and then create a new case. ## CGWUploadFile A \*.vcf file needs to be uploaded to initial the jobs. Use this widget to upload a \*.vcf file. A case needs to be created first for this widget to work. ## CGWJob One or more CGW jobs can be created for one sample. Each section of CGWJob can create one job. Before creating a CGW job, a CGW case need to be created and a \*.vcf file need to be uploaded first. ### Create a job Click **Create a job** button to create a job. Once a job is created, the job id will be assigned to the job id. ### Cancel a job Once a job is created, it can be canceled by clicking **Cancel Job** button. {% hint style="info" %} Note: Currently, the CGW API to cancel job is not working. {% endhint %} ### Check report Once a job is generated, the job will start running immediately. It will take around two hours to finish the CGW scripts. You can use the button **Check report** to check if the report is complete. If it is complete, a report id will be assigned and you will have the option to download the report. ### Download report Once a report is completed, the report can be downloaded via clicking Download report button. The report is generated in PDF format, and zipped in a package **\[Report Id].pdf.gz**. ## CGW Workflow To start a CGW analysis, please follow these steps. This workflow assumes you have configured everything in [Before starting](#before-starting). 1. Add a new sample, fill in all necessary information. 2. [Create a new case](#create-a-case) from **Case** column. 3. [Upload a \*.vcf file](#cgwuploadfile) from **Analysis related files** column. 4. Add a new section with widget CGWJob (optional, such section will be created automatically if correctly configured in the [default sections](#default-sections)). 5. [Create a new job](#create-a-job). 6. [Check the report](#check-report). 7. [Download the report](#download-report). --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.labii.com/widgets/section-widgets/combination/cgw.md?ask=