Updated analysis: histologies MYCN status

[ewafula]

What analysis module should be updated and why?

Update OpenPedCan histologies with correct MYCN status from TARGET and GMKF clinical files

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

1. Add code at the end add_v11_updates.py script in the v11-OpenPedCan histologies update module to update the TARGET and GMKF tumor samples (sampe_type == Tumor) with MYCN status in the molecular_subtype and pathology_free_text_diagnosis columns of the `v11/histologies.tsv file using the cohort level mapping file attached below in this ticket
2. Recreate the cohort level histologies files for TARGET and GMKF by re-running the OpenPedCan_cohort_histologies module using the updated v11/histolgies.tsv file in step 1 above. The TARGET and GMKF updated cohort histologies file will have the updated pathology_free_text_diagnosis column while the molecular_subtype column will be set to all NAs.
3. Upload updated TARGET and GMKF cohort histologies files to Data Tracker

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

target_patient_clinical_mycn_status.tsv.zip
gmkf_patient_clinical_mycn_status.tsv.zip

When do you expect the revised analysis will be completed?

1/2

Who will complete the updated analysis?

@ewafula

[chinwallaa]

@jharenza to review