minor changes lab3

Signed-off-by: Sean Smith <[email protected]>

Author: Sean Smith

content/05-cicd-pipeline/02-codecommit-repo.md

@@ -41,12 +41,12 @@ Verify **echo $REPOURL** outputs a repo url like **https://git-codecommit.\<regi
 7. Clone the repository in your Cloud9 terminal and cd into it:
 
 ```bash
-$ git clone $REPOURL
-$ cd MyDemoRepo/
+git clone $REPOURL
+cd MyDemoRepo/
 ```
 You can ignore the warning shown [*warning: You appear to have cloned an empty repository*]
 
 8. Now let's update the default branch from **master** to **main**:
 ```
-$ git branch -m master main
+git branch -m master main
 ```

content/05-cicd-pipeline/03-docker-buildspec.md

@@ -13,10 +13,10 @@ In this section, you will create a Docker container for the application and a bu
 A [buildspec](https://docs.aws.amazon.com/codebuild/latest/userguide/build-spec-ref.html) is a collection of build commands and related settings in YAML format. This file is used by [AWS CodeBuild](https://docs.aws.amazon.com/codebuild/latest/userguide/welcome.html) to automatically create an updated version of the container upon code changes. The buildspec file informs CodeBuild of all the actions that should be taken during a build run for your application. In the next section, you will dive deeper on what is CodeBuild and how to set it up as part of a pipeline. 
 
 
-1. Confirm you are in the **MyDemoRepo** repository, if not enter into it:
+1. Confirm you are in the **MyDemoRepo** repository:
 
-```bash
-cd MyDemoRepo
+```
+pwd # should be MyDemoRepo
 ```
 
 2. Create a Docker container for the application. We're going to use the [Amazon Linux container](https://gallery.ecr.aws/amazonlinux/amazonlinux) from [Amazon Elastic Container Registry (ECR) Public Gallery](https://docs.aws.amazon.com/AmazonECR/latest/public/public-gallery.html).

content/05-cicd-pipeline/06-updatebuild.md

@@ -12,9 +12,10 @@ We will modify the Dockerfile to run a Genomics workflow using [Nextflow](https:
 We will go over the Nextflow architecture and job execution/orchestration more in the next lab. For now, we will go ahead and update the repository and see how the CICD pipeline works for your build.
 
 
-1. Go to the CodeCommit repository created in your **Cloud9** environment
-```bash
-cd MyDemoRepo
+1. First confirm you are in the **MyDemoRepo** repository:
+
+```
+pwd # should be MyDemoRepo
 ```
 
 2. Update the Dockerfile to the following. This is an entrypoint script which can consume the link to an Amazon S3 bucket or a git repository from which to download the Nextflow pipeline and executes it.
@@ -58,12 +59,14 @@ git push origin main
 5. In the AWS Management Console search bar, type and select **CodePipeline**. Click on the **MyDemoPipeline** that you created in the previous section. You should now see that the CodeCommit push above should have triggered the build via CodeBuild automatically. 
 ![AWS CodePipeline](/images/cicd/codepipeline-6.png)
 
-6. Click on the AWS CodeBuild deep link from the Build stage of the CodePipeline. This will take you to the CodeBuild project that you created. Click on the latest build in **Build history** and examine the **Build logs**.
+6. Click on the **Details** deep link from the Build stage of the CodePipeline. This will take you to build logs from the CodeBuild project that you created:
+
 ![AWS CodePipeline](/images/cicd/codepipeline-7.png)
+![AWS CodePipeline](/images/cicd/codepipeline-8.png)
 
 
 7. Click on the **Tail logs** to see the on-going or completed build process. This is showcasing every step of the build process as provided in your **buildspec.yml** file.
-![AWS CodePipeline](/images/cicd/codepipeline-8.png)
+![AWS CodePipeline](/images/cicd/codepipeline-9.png)
 
 8. In addition to the build the pipeline is also pushing the built container image to the container registry in Amazon ECR.