v12 cnv and fusion frequencies

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update cnv-frequencies and fusion-frequencies modules with v12 data and change the output column for somatic_mutation to pediatric_cancer

What was your approach?

Change datatypeId column value for the output table from somatic_mutation to pediatric_cancer

What GitHub issue does your pull request address?

d3b-center/ticket-tracker-OPC#527
d3b-center/ticket-tracker-OPC#528

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

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.

[kelseykeith]

Overall this looks great!

• Except for the PMTL column in the cnv-frequencies table (see Issues below), the structure of the new v12 tables for both modules match the v11 version.
• The data mostly match except for adjustments made with the new release.
• The fusion-frequencies module has been updated to use the DGD fusions in the data/ directory, not the file inside the module
• The datatypeId column was correctly updated in both modules.

Minor Issues:

• @ewafula, the PMTL annotation is being removed in v12 correct? So it's right that it's missing from the cnv-frequencies table when it was present in v11.
• I suggested removing the .gitignore in the fusion-frequencies module since the files are all under 10Mb, well under GitHub's file size limit of 100Mb, but if we're moving away from this model it can be left alone

[ewafula]

Overall this looks great!

• Except for the PMTL column in the cnv-frequencies table (see Issues below), the structure of the new v12 tables for both modules match the v11 version.
• The data mostly match except for adjustments made with the new release.
• The fusion-frequencies module has been updated to use the DGD fusions in the data/ directory, not the file inside the module
• The datatypeId column was correctly updated in both modules.

Minor Issues:

• @ewafula, the PMTL annotation is being removed in v12 correct? So it's right that it's missing from the cnv-frequencies table when it was present in v11.
• I suggested removing the .gitignore in the fusion-frequencies module since the files are all under 10Mb, well under GitHub's file size limit of 100Mb, but if we're moving away from this model it can be left alone

@kelseykeith, that is correct PMTL is no longer in all MTP tables. All MTP were all updated to exclude PMTL in a previous PR.

[kelseykeith]

Thanks for the changes @zzgeng! This looks good now, approved