Remove any variant type #5219
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Remove any variant type #5219
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northwestwitch
commented
Feb 6, 2025
| multiple=True, | ||
| help="Type of analysis", | ||
| ) | ||
| @click.option("--rank-threshold", type=click.INT, default=5, help="With rank threshold lower than") | ||
| @click.option("--variants-threshold", type=click.INT, help="With more variants than") | ||
| @click.option( |
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New option, mutually exclusive with --keep-ctg
northwestwitch
commented
Feb 6, 2025
| @@ -23,8 +24,18 @@ | |||
| "Total variants", | |||
| "Removed variants", | |||
| ] | |||
| VARIANT_CATEGORIES = list(VARIANTS_TARGET_FROM_CATEGORY.keys()) + ["wts_outliers"] | |||
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["wts_outliers"] is added like that, because these variants are on another collection (omics_variant).
northwestwitch
commented
Feb 6, 2025
| @@ -68,15 +86,16 @@ | |||
| @with_appcontext | |||
| def variants( | |||
| user: str, | |||
| case_id: list, | |||
| case_id: tuple, | |||
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These are all tuples, I've actually checked
added 2 commits
February 6, 2025 13:52
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #5219 +/- ##
=======================================
Coverage ? 84.41%
=======================================
Files ? 326
Lines ? 19860
Branches ? 0
=======================================
Hits ? 16765
Misses ? 3095
Partials ? 0 ☔ View full report in Codecov by Sentry. |
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This PR adds a functionality or fixes a bug.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: