IGB is able to download the artifacts from the newly added nexus repository,
Steps followed,
1. Deleted the HTSJDK and BigWig artifacts from the local repository to trigger the download.
2. Executed maven clean install
3. Verified if the artifacts downloaded successfully.
The below logs also verify the same.

Downloading from repo1: http://maven.bioviz.org/repo1/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
Downloading from repo2: http://maven.bioviz.org/repo2/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
Downloading from repo3: http://maven.bioviz.org/repo3/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
[WARNING] Could not validate integrity of download from https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar: Checksum validation failed, no checksums available
[WARNING] Checksum validation failed, no checksums available from maven-releases for https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar
Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.1/htsjdk-igb-2.16.1.jar (1.6 MB at 352 kB/s)

Downloading from repo1: http://maven.bioviz.org/repo1/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
Downloading from repo2: http://maven.bioviz.org/repo2/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
Downloading from repo3: http://maven.bioviz.org/repo3/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar
Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/broad/igv/bigwig/2.0.0/bigwig-2.0.0.jar (75 kB at 264 kB/s)

At this time this issue can be marked Done.
Please reopen in case of any other issues found.

I'm concerned about the warning message above for the htsjdk artifact.
We should provide the checksum so that client programs can verify the artifact upon download.
That's because some clients/IDEs may not trust artifacts that don't have checksums and therefore can't be verified.
I uploaded this artifact "by hand" using the Nexus3 GUI. I would have expected the checksum files would be generated upon upload.
I searched for information about this and found this issue from the Nexus vendor:

• https://issues.sonatype.org/browse/NEXUS-16493
  Looks like this is a missing feature in our version of Nexus. We are running Nexus 3.10. Fix appears to have been released with 3.11.

Let's do this for the next steps:

• Add code to our gradle.build script for uploading to our nexus repository. For example for how to do this, see the gradle.build file in our bigwig repository - https://bitbucket.org/lorainelab/bigwig
• Please add the code to the end of the file; I'm pretty sure it can co-exist with the htsjdk project's current upload code, which hard-codes their repository address. Maybe call our upload function "uploadArtifactsToIgbRepo" (??)
• You can test the upload process using our Nexus repository's "testuser" user, which has write permission to a test maven repositor - https://nexus.bioviz.org/repository/Test_IGB_Artifact_Deployment/ (Ask Kiran for details, or Dr. Loraine)

When it's working, I will need to upload it to our maven-releases repository, which is used the IGB project.

Also, we should upgrade to the newest version of Nexus repository code. Whoever does this will need credentials to access the host. (Ask me.)
Documentation:
https://support.sonatype.com/hc/en-us/articles/115000350007?_ga=2.143644791.35725550.1540530730-460053495.1540530730