Add support to run raredisease with WES #3232

rannick · 2024-05-15T08:57:21Z

Description

Added

Support sending exomes cases in raredisease

Changed

Default target bed file for both MIP and raredisease updated to "twistexomerefseq_10.2_hg19_design.bed"

Fixed

How to prepare for test

Ssh to relevant server (depending on type of change)
Use stage: us
Paxa the environment: paxa

Install on stage (example for Hasta):

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

Do ...

Expected test outcome

Check that ...
Take a screenshot and attach or copy/paste the output.

Review

Tests executed by
"Merge and deploy" approved by
Thanks for filling in who performed the code review and the test!

This version is a

MAJOR - when you make incompatible API changes
MINOR - when you add functionality in a backwards compatible manner
PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

Document in ...
Deploy this branch on ...
Inform to ...

cg/meta/workflow/nf_analysis.py

cg/meta/workflow/raredisease.py

tests/cli/workflow/nf_analysis/test_cli_config_case.py

Co-authored-by: Vadym <[email protected]>

…mics/cg into raredisease-exomes

henrikstranneheim

Nice!

cg/constants/constants.py

cg/meta/workflow/nf_analysis.py

tests/conftest.py

Co-authored-by: Henrik Stranneheim <[email protected]>

rannick · 2024-05-23T11:05:49Z

@ivadym @henrikstranneheim: ready for re-review!

ivadym

Nice! Looks good!

cg/meta/workflow/analysis.py

Co-authored-by: Vadym <[email protected]>

cg/meta/workflow/analysis.py

Co-authored-by: Vadym <[email protected]>

…ed_cases into AnalysisAPI as used by non-nf workflows

ivadym

💯 💯 💯

cg/meta/workflow/analysis.py

Co-authored-by: Vadym <[email protected]>

sonarqubecloud · 2024-05-27T07:41:51Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

rannick · 2024-05-27T08:40:48Z

Deployment to prod:

bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-prod.sh -e P_cg -t cg -b master -a
Collecting git+https://github.com/Clinical-Genomics/cg@master
  Cloning https://github.com/Clinical-Genomics/cg (to revision master) to ./tmp/pip-req-build-w_tj8vjs
  Running command git clone --quiet https://github.com/Clinical-Genomics/cg /home/hiseq.clinical/tmp/pip-req-build-w_tj8vjs
  Resolved https://github.com/Clinical-Genomics/cg to commit e53957902e573ae6b977aecfab03c58864ee00ec
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: cg
  Building wheel for cg (pyproject.toml) ... done
  Created wheel for cg: filename=cg-60.8.11-py3-none-any.whl size=3722315 sha256=612750b2d7afe70938d590dae9bccee25e07ad385fac5c1350dd9eed9b95197f
  Stored in directory: /home/hiseq.clinical/tmp/pip-ephem-wheel-cache-wuntc1v2/wheels/70/a8/7b/4abe0a2bf6472156279388f2b6206b4edcafc346e623de2208
Successfully built cg
Installing collected packages: cg
  Attempting uninstall: cg
    Found existing installation: cg 60.8.10
    Uninstalling cg-60.8.10:
      Successfully uninstalled cg-60.8.10
Successfully installed cg-60.8.11
Collecting git+https://github.com/Clinical-Genomics/cg@master
  Cloning https://github.com/Clinical-Genomics/cg (to revision master) to ./tmp/pip-req-build-e63ru812
  Running command git clone --quiet https://github.com/Clinical-Genomics/cg /home/hiseq.clinical/tmp/pip-req-build-e63ru812
  Resolved https://github.com/Clinical-Genomics/cg to commit e53957902e573ae6b977aecfab03c58864ee00ec
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
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fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/hiseq.clinical
done.
Log deploy... done.
cg, version 60.8.11
remote: Enumerating objects: 50, done.
remote: Counting objects: 100% (45/45), done.
remote: Compressing objects: 100% (31/31), done.
remote: Total 50 (delta 24), reused 18 (delta 13), pack-reused 5
Unpacking objects: 100% (50/50), done.
From https://github.com/Clinical-Genomics/cg
   bf35bfd..e539579  master     -> origin/master
   3fe1ca3..28dfbc6  add-pacbio-smrt-cell-model -> origin/add-pacbio-smrt-cell-model
   557ee26..8efa25b  parse-into-sequencing-run -> origin/parse-into-sequencing-run
   a35b022..e8687a9  patch_taxprofiler_versions -> origin/patch_taxprofiler_versions
 * [new branch]      point-run-paramters-to-flow-cell -> origin/point-run-paramters-to-flow-cell
 * [new tag]         v60.8.11   -> v60.8.11
Already on 'master'
Your branch is behind 'origin/master' by 2 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating bf35bfd..e539579
Fast-forward
 .bumpversion.cfg                                 |   2 +-
 cg/__init__.py                                   |   2 +-
 cg/constants/constants.py                        |   2 +-
 cg/meta/workflow/analysis.py                     |  40 +++++++++++++++++++++--------
 cg/meta/workflow/nf_analysis.py                  |  15 +++--------
 cg/meta/workflow/raredisease.py                  |  25 +++++++++++++++----
 cg/models/raredisease/raredisease.py             |   9 ++++++-
 pyproject.toml                                   |   2 +-
 tests/cli/workflow/nf_analysis/test_cli_start.py |   1 +
 tests/conftest.py                                | 138 ++++++++++++++++++++++++++++++++++++++++++++++++++++-------------------------------------------------
 tests/meta/workflow/test_raredisease.py          |   5 +++-
 11 files changed, 140 insertions(+), 101 deletions(-)
/home/hiseq.clinical
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.

rannick added 9 commits May 15, 2024 10:55

add analysis_type and target_bed to config file

255076f

fix typo and linting

d602e2e

add new params to workflow params

e4012b3

fix parameters

bbb60ea

add default setting

db785d5

add error raising and mock lims access in test

e6c51c9

add mock lims access for all necessary tests

d9e75bf

black

970bc25

add mock lims access for all necessary tests

3219aa5

rannick self-assigned this May 15, 2024

rannick marked this pull request as ready for review May 15, 2024 15:31

rannick requested a review from a team as a code owner May 15, 2024 15:31

Merge branch 'master' into raredisease-exomes

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rannick and others added 10 commits May 16, 2024 20:06

Update cg/meta/workflow/nf_analysis.py

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Update cg/meta/workflow/raredisease.py

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Update cg/meta/workflow/raredisease.py

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Update tests/cli/workflow/nf_analysis/test_cli_config_case.py

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remove duplicate definition of raredisease_context

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test with mocker part of fixture

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Merge branch 'raredisease-exomes' of https://github.com/Clinical-Geno…

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henrikstranneheim reviewed May 23, 2024

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rannick and others added 5 commits May 23, 2024 10:28

Update cg/meta/workflow/nf_analysis.py

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Update tests/conftest.py

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typing and moving to analysisAPI

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fix merge conflicts

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rannick added 4 commits May 23, 2024 12:08

use statusDB to extract analysis type

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remove redundant mocker

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use optional string

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Merge branch 'master' into raredisease-exomes

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Merge branch 'master' into raredisease-exomes

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move get_target bed to RarediseaseAnalysisAPI

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move get-

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Update cg/meta/workflow/analysis.py

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add error message

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move is_multiple_samples_allowed into analysisAPI to have get_validat…

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…ed_cases into AnalysisAPI as used by non-nf workflows

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Merge branch 'master' into raredisease-exomes

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Merge branch 'master' into raredisease-exomes

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rannick merged commit 5b90cde into master May 27, 2024
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rannick deleted the raredisease-exomes branch May 27, 2024 07:47

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Add support to run raredisease with WES #3232

Add support to run raredisease with WES #3232

rannick commented May 15, 2024 •

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rannick commented May 27, 2024

Add support to run raredisease with WES #3232

Add support to run raredisease with WES #3232

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rannick commented May 15, 2024 • edited Loading

Description

Added

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Fixed

How to prepare for test

How to test

Expected test outcome

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sonarqubecloud bot commented May 27, 2024

Quality Gate passed

rannick commented May 27, 2024

rannick commented May 15, 2024 •

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