Create methyl array probes annotation module

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Create Illumina Infinium Human Methylation array probe annotation based on the Human Build 38 (GRCh38/hg38) and GENCODE v39 release

What was your approach?

Created OPC module for generating methyl probe annotations

What GitHub issue does your pull request address?

• Updated analysis: methylation summary - add details on probe liftover #385

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

• Review the entire module code
• Description of the analysis process in README
• Docker file update to include installation of module dependencies

Is there anything that you want to discuss further?

No

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

tables

What is your summary of the results?

• results/infinium.gencode.v39.probe.annotations.bedtools.tsv.gz
• results/infinium.gencode.v39.probe.annotations.tsv.gz

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

minor, but i see there is a typo in script 02 - "interect" should be "intersect".

[rjcorb]

The module runs successfully when suggested modifications are made

[ewafula]

The module runs successfully when suggested modifications are made

Thank you, @rjcorb, for reviewing

[ewafula]

@jharenza, @rjcorb, updated bash script check to check if Illumina methyl array probe manifest exists, and downloads from data release s3 bucket if it doesn't exist.

[jharenza]

Note: this is awaiting updates based on some feedback @afarrel will provide

[jharenza]

From @afarrel via slack:

Gene feature annotations of methylation probes located downstream of the 3'UTR (as annotated by GTF file) should be changed from 3'UTR to either "3' downstream" or "3' downstream region" (Or something more suitable)

[ewafula]

@afarrel, PR updated - 3'-UTR 1kb extension added as an additional feature to the probe annotations as you suggested.

Cc @jharenza

[afarrel]

Thanks @ewafula! Everything looks good.