Update analysis modules to use GENCODE 39 - N/2

[ewafula]

What analysis module should be updated and why?

tp53_nf1_score - currently using GENCODE v27

What changes need to be made? Please provide enough detail for another participant to make the update.

Update OpenPedcan analysis modules listed above that utilize older GENCODE versions, where required, to match GENCODE v39 currently on the MPT portal and regenerate analysis results for each module.

• Original issue ticket

What input data should be used? Which data were used in the version being updated?

Module-specific inputs, including v11 OpenPedCan datasets and GENCODE v39 GTF, which are downloaded into the local repo
data/ directory with the download-data.sh script.

When do you expect the revised analysis will be completed?

To updated during the next sprint

Who will complete the updated analysis?

@rjcorb

[ewafula]

@rjcorb , you can use grep -r 'gencode' * within the module directory to determine the files and scripts that need updating. These simple updates will give you a general understanding of OpenPedCan module development, execution, datasets, and structure, which will be helpful in the future when developing a module or reviewing a pull request

[ewafula]

@rjcorb, you don't have to update snv-callers module. It is no longer used.