Custom output format files

inodb commented 2 years ago

Allow changing the column names etc using a supplied output format file

Some of the output formats could be:

[ ] tcga: https://docs.cbioportal.org/file-formats/#extended-maf-format. List all 37 first and anything extra goes in the back alphabetically
[ ] minimal: whatever was inputted and newly annotated columns by genome nexus
[ ] gdc: ??? Not sure what this should be yet. (They might have a few additional columns beyond tcga, 126 columns)
[ ] any custom ordering of columns (already implemented)

ozguzMete commented 2 years ago

https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/198

magically removing empty columns is much more difficult hence the data is row-based. Doable but painful... if the output format is enough for most of the time, we can skip this part

ozguzMete commented 1 year ago

I have added tcga and minimal to the #198

genome-nexus / genome-nexus-annotation-pipeline

Custom output format files #194