[ENH] ClinSV v1.1.0 - Githubissues

J-Bradlee commented 2 years ago

Description

Implementation of a few features that will make ClinSV more robust and efficient.

Features to be implemented:

[x] Currently unable to switch between hs37d5 and grch38 on the fly, must use version 0.9 for hs37d5 and version 1.0 for grch38. Ideally we want to have one version of ClinSV to be able to easily switch between the two. Dedicated issue at #28 .
[x] Currently there is no support for hg19 style chromosome names for v37 or v38 reference genomes. We should provide support for this. Dedicated issue at #31 .
[ ] Not all resources available to ClinSV are being used. It is currently hard coded as some preset values. We want to be able to have ClinSV dynamically use resources available to speed up the computation.
[x] Have the Docker file pull all the ClinSV scripts directly from the main git, rather than using manually generated gzip folder of the scripts.

Bug fixes

[ ] #61

Misc updates

[x] Update download links with ccia bucket, for more reliable data storage.

drmjc commented 2 years ago

Thanks @J-Bradlee, this is a good summary of the scope of v1.1.0

If the Docker/clinsv_scripts.tar.gz file includes a copy of the files in the scripts/* folder, can you drop the need for the clinsv_scripts.tar.gz file in this release too?

J-Bradlee commented 2 years ago

Good point @drmjc I'll change up the docker file to pull directly from git, so we no longer need to have the zip files.

J-Bradlee commented 1 year ago

Current dev docker container with these completed features can be pulled by

docker pull mrbradley2/clinsv:v1.1-dev

EricDeveaud commented 1 year ago

seems to me that https://github.com/KCCG/ClinSV/commit/18e7603293947ac49f4e82233e40202a92aa19b4

should be applied to 1.1-dev branch to

KCCG / ClinSV

[ENH] ClinSV v1.1.0 #27

Description

Features to be implemented:

Bug fixes

Misc updates