Test call to config case fails - #4710

Open

mogmi wants to merge 78 commits into

test-config-case-fails

Commits on Jul 24, 2025

Commits on Jul 25, 2025

dev(Balsamic Start) Add Balsamic launch command (#4525)
Vince-janv
authored
b1e4d3f

Commits on Jul 28, 2025

dev(Balsamic Start) Add tracker (#4526)
Vince-janv
authored
b7d2ea9

Commits on Jul 29, 2025

dev(Balsamic Start) Add Balsamic to AnalysisStarterFactory (#4531)
Vince-janv
authored
7b5db74
dev(balsamic start) Add dev commands (#4533)
Vince-janv
authored
52dde7f

Commits on Jul 31, 2025

Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
0919ca2
re-run black
diitaz93
committed
3f70ab7

Commits on Sep 30, 2025

dev(Balsamic) Address bugs in CLI (#4535)
Vince-janv
authored
2392d7a
Merge master, and conform to new CLI-dumping method
Vince-janv
committed
c8ff596
Add config changes to integration test file
Vince-janv
committed
ff3b020

Commits on Oct 6, 2025

Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
ac8e70a
fix failing tests in conflict merge
diitaz93
committed
c651b6e

Commits on Oct 13, 2025

Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
76ae954
Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
b19ab43

Commits on Oct 20, 2025

Add loqusdb dump files (#4633)

authored
d2eea97
Merge branch 'master' into dev-new-start-balsamic
islean
authored
9ee163c
Fix test
islean
committed
c54692d
Fix integration test
islean
committed
79158d0
address type hint comments
diitaz93
committed
e32946b

Commits on Oct 21, 2025

Start working in configurator factory
islean
committed
2bb8afd
WIP
mogmi
committed
e722feb
Test implemented
RasmusBurge-CG
committed
13f080c
WIP - tests analysis starter factory
diitaz93
committed
ff3ad79
Add Balsamic to analysis starter test
islean
committed
0b935d1
WIP
mogmi
committed
9c2a93f
WIP
RasmusBurge-CG
committed
f7e78c7
WIP - clearing to-dos
diitaz93
committed
e647e28
Start on start test
islean
committed
72ee086
WIP
mogmi
committed
2eb5391
Green state
RasmusBurge-CG
committed
0be19ad
WIP - test flags
diitaz93
committed
c1d1696
Start on start test
islean
committed
853fc8a
Test cases with male and unknown samples (#4659)
mogmi
authored
5b0a8c8
Add dev CLI tests
diitaz93
committed
2f4af56
Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
8404db6

Commits on Oct 22, 2025

Add a TODO
islean
committed
e70c8fb
WIP
mogmi
committed
4d2f1bb
WIP
RasmusBurge-CG
committed
1b9283e
WIP workflow profile
diitaz93
committed
07883d2
Fix workflow profile
islean
committed
171c0f7
WIP
mogmi
committed
fdd0b5e
WIP
RasmusBurge-CG
committed
72a0ac0
added head-job profile
diitaz93
committed
5a6269f
Remove benchmark and mail-user
RasmusBurge-CG
committed
bba93ed

Commits on Oct 23, 2025

Test balsamic start command (#4664)
mogmi
authored
816f8b0

Commits on Oct 24, 2025

Add loqusdb dump file second attempt (#4663)

authored
5ecd2fd
Merge branch 'master' into dev-new-start-balsamic
islean
authored
ec7456b
Change expected commands in integration tests to match Balsamic v18 (#4668)
mogmi
authored
6714249
Adress comments
RasmusBurge-CG
committed
4f61c10
Address comments
RasmusBurge-CG
committed
0260087
Address comments
RasmusBurge-CG
committed
4713edd
Address comments
RasmusBurge-CG
committed
cabd41f
Address comments
RasmusBurge-CG
committed
90f054f
Address comments
RasmusBurge-CG
committed
e6e1f72
Address comments
RasmusBurge-CG
committed
527d5a1
Update tests/cli/workflow/balsamic/test_cli_balsamic.py

RasmusBurge-CG
and
diitaz93
authored
b4eb6b5
Update tests/cli/workflow/balsamic/test_cli_balsamic.py

RasmusBurge-CG
and
diitaz93
authored
905f96c
Update tests/cli/workflow/balsamic/test_cli_balsamic.py

RasmusBurge-CG
and
diitaz93
authored
7a10d89
Address comments
RasmusBurge-CG
committed
53e863d
Merge remote-tracking branch 'origin/dev-new-start-balsamic' into dev-new-start-balsamic
RasmusBurge-CG
committed
9d41e59

Commits on Oct 27, 2025

Pass fastq path from fastq handler to config file creator
diitaz93
committed
2cae80e
Refactor fastq path owner
islean
committed
6c8183c
Rename method
islean
committed
fe926d5

Commits on Nov 5, 2025

Activate the configured conda environment when starting the analysis (#4690)
mogmi
authored
f05b02a

Commits on Nov 6, 2025

Fix real store test balsamic (#4673)

diitaz93
and
islean
authored
9703713

Commits on Nov 7, 2025

Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
d8806f2

Commits on Nov 10, 2025

Balsamic dev commands integration test (#4693)
mogmi
authored
31726d2
Merge branch 'master' into dev-new-start-balsamic
diitaz93
committed
e5a8221

Commits on Nov 11, 2025

order fixtures
diitaz93
committed
c8ab97d
Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
632d8d8

Commits on Nov 13, 2025

Patch balsamic config2 (#4707)

authored
402226f
Merge branch 'master' into dev-new-start-balsamic
diitaz93
authored
267676a
WIP - test for failing balsamic command
diitaz93
committed
0d40fa5
Finished test and implementation
islean
committed
4e477f6
Log balsamic error from config case command
mogmi
committed
3f73647
Fix exome flag order
islean
committed
7f4f1b9
Use named function to test check=False and logging Balsamic error output
mogmi
committed
05c11f9