This PR deprecates the command line option --finngen-annotation-version, previously used to tell the script how the fg annotation file is structured. Since the releases have rolled by and the old file structure is not really used, this option is pretty much useless.
This PR specifically
1) removes the command-line option
2) removes the handling for the old version, and prints a warning in case the file seems not to match the current one
3) updates README
4) updates the wdl pipeline and docker.
Relevant issue: #126
This PR deprecates the command line option
--finngen-annotation-version, previously used to tell the script how the fg annotation file is structured. Since the releases have rolled by and the old file structure is not really used, this option is pretty much useless.This PR specifically 1) removes the command-line option 2) removes the handling for the old version, and prints a warning in case the file seems not to match the current one 3) updates README 4) updates the wdl pipeline and docker.