Prof. [~aloraine], I was successfully able to build the app without parent reference.
The problem is for some of IGB dependencies, it is referring following repository:
http://maven.bioviz.org/repo2/org/lorainelab/igb/
Which has 9.0.0 version of all the JARs. Whereas, the current version of most of the JARs under IGB is 9.1.0.
Will it make any difference? If yes then do we need to update the repository?

I have tested the app whose pom.xml has parent reference with the one in the separate repository.
Both apps generated a bed file which are identical.
Pushing the changes made in pom.xml to the master.
Steps for testing:
1) Clone the repository on your machine.
2) run mvn install command for the same.
3) Go to the target folder.
4) Unpack the jar file and check if the git.properties file is there on not.
5) If it is there then check if the file shows proper commit hash and repository metadata details or not.
6) Also, on the IGB platform go to Tools>Open App Manager
7) Click on Manage Repositories and add the target folder path of your newly built app which has repository.xml. Click Done.
8) Install 23andMe SNP Converter.
9) Check to run the converter steps. You can use sample 23andMe data file which is present under src>test>resources folder.
10) Compare the generated .bed file with the one which is geneated using the 23andMe SNP Converter app which is built under IGB repository.

Thanks for setting up the bitbucket pipeline!

I have a followup question about: bitbucket-pipelines.yml

• I noticed that the two branches pipelines look identical. Also, I noticed that only the default pipeline deploys to the Downloads directory. Can we get rid of the two branches profiles and instead just use the default pipeline?

Another question:

• The pom.xml refers to a non-existant directory - <copy file="$ {project.build.directory}

  /$

  {project.build.finalName}

  .jar" todir="$

  {basedir}

  /../../extbundles/optional"/>
  How is this working? Can it really be built?

Done with the simplification of pom.xml and pipeline configuration file for the app.
You can review the changes present at:
https://bitbucket.org/lorainelab/23andme-snp-converter/src/master/pom.xml
https://bitbucket.org/lorainelab/23andme-snp-converter/src/master/bitbucket-pipelines.yml