Missing germline sex estimate in ops csv

[jharenza]

What data file(s) does this issue pertain to?

https://github.com/d3b-center/histologies-qc/blob/main/histologies/20230310_release_histologies_ops.csv

What release are you using?

v12 OPC

Put your question or report your issue here.

missing_germline_sex.csv

[zhangb1]

@HuangXiaoyan0106 can you check this?

[jharenza]

missing_germline_sex.csv Current update ^ using the file in https://cavatica.sbgenomics.com/u/d3b-bixu-ops/monthly-release-data/files/#q?path=20230515_release (cc @HuangXiaoyan0106 @zhangb1 @aadamk)

[HuangXiaoyan0106]

missing_germline_sex.csv Current update ^ using the file in https://cavatica.sbgenomics.com/u/d3b-bixu-ops/monthly-release-data/files/#q?path=20230515_release (cc @HuangXiaoyan0106 @zhangb1 @aadamk)

I checked them and none of them are on the master genomics manifest. cc @zhangb1

[HuangXiaoyan0106]

Hi @jharenza, here is the new histology file with the missing gender added based on the extra Hope manifest provided by @zhangb1 https://cavatica.sbgenomics.com/u/d3b-bixu-ops/monthly-release-data/files/64644258301b36722425cfbe/

[jharenza]

thanks so much @HuangXiaoyan0106 - is it possible in the future to name this file without a date and extra text? That way we do not have to change the filename everytime we generate a histologies file for a data release? Wondering if maybe you can have a "current" folder or something where that filename is always the same and the dated ones are archived elsewhere? Not sure if this would work for you?

[HuangXiaoyan0106]

@jharenza Currently, we do not have this function. But I can mark this on my to-do list, I need to think about the whole process of Airflow. If this feature is implemented, I will let you know.

[jharenza]

thanks, just putting it out there! also, looks like the file is good, will close.