Updating module per latest v12 successful run on HPC

[sangeetashukla]

Purpose/implementation Section

Update the module scripts to ensure the changes made for v12 are captured in the final OPC repo

What scientific question is your analysis addressing?

Capture the process and scripts for executing a differential expression analysis between tumor and normal samples in pairs for each Disease(cancer_group) and Dataset(cohort) combination.

What was your approach?

• Update column names as below:
  cohort --> Dataset
Gene_Ensembl_ID --> targetFromSourceId
EFO --> diseaseFromSourceMappedId
cancer_group --> Disease
cancer_group_Count --> Disease_Count
cancer_group_MeanTpm --> Disease_MeanTpm

• Make appropriate script changes and add a new script to perform a QC and ensure all the result tables are successfully generated. In case of failure, the script must also capture information on which tables were not generated.

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

This PR captures the script changes as described above, and the result of the QC script that also performs a spot check on the results produced, so that downstream analysis is more accurate.

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)?

What is your summary of the results?

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.

[ewafula]

@sangeetashukla, thanks for updating. This reflects the changes we discussed, and you made on the tumor-normal DESeq2 module while working to release the v12 MTP tables.