Updated analysis: update fusion-frequencies for v11 data release

[logstar]

What analysis module should be updated and why?

After v11 data is released, fusion-frequencies module needs to be updated to generate the following files using v11 data:

• analyses/fusion-frequencies/results/putative-oncogene-fused-gene-freq.jsonl.gz
• analyses/fusion-frequencies/results/putative-oncogene-fused-gene-freq.tsv.gz
• analyses/fusion-frequencies/results/putative-oncogene-fusion-freq.jsonl.gz
• analyses/fusion-frequencies/results/putative-oncogene-fusion-freq.tsv.gz

The JSONL files will be used to update MTP for OpenPedCan-analysis v11 data release.

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

• Download v11 data.
• Rerun fusion-frequencies module.
• If any assertion fails, handle the failed assertion.

@jharenza - I wonder if there is any v11 data specific changes that need to be made to the fusion-frequencies module.

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

Input data for fusion-frequencies module.

v11 data release needs to be used.

When do you expect the revised analysis will be completed?

1 week.

Who will complete the updated analysis?

cc @chinwallaa @taylordm @ewafula

[jharenza]

@jharenza - I wonder if there is any v11 data specific changes that need to be made to the fusion-frequencies module.

For v11, we have fusion-dgd.tsv.gz which contains fusion calls for DGD data. We should add this to the table as its own cohort, but do not add this cohort to "All cohorts".

[jharenza]

@sangeetashukla for this update, can you also rename "DGD" to "CHOP P30 panel" please? cc @afarrel

[jharenza]

closing with https://github.com/PediatricOpenTargets/OpenPedCan-analysis/pull/233