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TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis #2190

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TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis #2190

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@jtarraga jtarraga commented Nov 10, 2022

Remove HS metrics from alignment QC.

jtarraga and others added 10 commits November 3, 2022 10:29
@jtarraga
analysis: update mutational signature to biodata changes, #TASK-2242,…
5d10e1b 
… #TASK-2243
@jtarraga
analysis: generate CLI automatically, #TASK-2242, #TASK-2243
5a58318
@jtarraga
analysis: major improvements in sample quality control (mutational si…
484776d 
…gnature) and generate CLI, #TASK-2242, #TASK-2243
@jtarraga
analysis: updae mutational signature query and generate CLI, #TASK-22…
eef1601 
…42, #TASK-2243
@jtarraga
analysis: add log message, #TASK-2242, #TASK-2243
7988a47
@jtarraga
analysis: raise an exception when running a mutational-signature-quer…
80bab76 
…y and the genome context file is not present, #TASK-2242, #TASK-2243
@jtarraga
analysis: save mutational signature and fitting (as data model files)…
cf969cb 
… in the job dir, and generate CLI, #TASK-2242, #TASK-2243
@jtarraga
Merge branch 'release-2.4.x' into TASK-2242
abd3897
@jtarraga
analysis: remove HS metrics from alignment QC analysis, and generate …
cd4c96c 
…CLI, #TASK-2303, #TASK-2304
@pfurio
app: add signature fitting migration, #TASK-2242
fedc4d3
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jtarraga commented Nov 10, 2022

Task linked: TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis

@jtarraga jtarraga changed the title TASK-2304 TASK-2304 Update the alignment QC to remove the hybrid selection (HS) metrics analysis Nov 10, 2022
juanfeSanahuja
juanfeSanahuja previously approved these changes Nov 11, 2022
View reviewed changes
juanfeSanahuja and others added 29 commits December 12, 2022 13:12
@juanfeSanahuja
Clean spaces
3a986c0
@juanfeSanahuja
Merge branch 'TASK-2390' of https://github.com/opencb/opencga into TA…
6ce48dd 
…SK-2390
@juanfeSanahuja
Port Patch Version 1.2.11 #TASK-2474
a564f12
@juanfeSanahuja
Port Patch Version 1.2.10.1 #TASK-2475
e59c6af
@jtarraga
Merge and resolve conflicts, #TASK-2242
beccef5
@jtarraga
Resolve conflicts, #TASK-2274
f18172b
@juanfeSanahuja
Port Patch Version 1.2.12 #TASK-2525
2c834d2
@jtarraga
analysis: fix some bugs and improve junit test, #TASK-2274, #TASK-2369
6189163
@pfurio
Merge pull request #2222 from opencb/TASK-2297
13fd25d 
TASK-2297 - Upgrade MongoDB version to 5.0.14
@pfurio
catalog: fix sample-individual association issue, #TASK-2539
74d985e
@imedina
core: fix Junit test
f960658
@pfurio
catalog: stop using old MongoClient, #TASK-2297
224c6e8
@pfurio
storage: remove opencga-storage-mongodb dependency, #TASK-2297
557f99f
@juanfeSanahuja
Check if the branch name begin per TASK-
99cc311
@juanfeSanahuja
Rebuild autogenerated code and merge develop
fb62379
@juanfeSanahuja
Merge pull request #2216 from opencb/TASK-2242
4087ef4 
TASK-2242 Improve mutational signature analysis
@imedina
Minor improvements in the dependency synchonisator
30d5606
@juanfeSanahuja
misc: sync_dependency.sh refactor to method update_library #TASK-2390
b0f75c6
@juanfeSanahuja
Update 'java-common-libs.version' dependency to 4.6.0-TASK-2390-SNAPSHOT
1f931af
@juanfeSanahuja
Update 'java-common-libs.version' dependency to 4.6.0-SNAPSHOT
329602d
@juanfeSanahuja
Merge branch 'develop' into TASK-2390
e613ec6
@j-coll
storage: Use dataRelease when calling to cellbase. #TASK-2575
74397e7
@jtarraga
Resolve conflicts (after merging develop), #TASK-2274
a909a13
@imedina
Merge branch 'TASK-2539' into develop
4514483
@j-coll
Merge pull request #2226 from opencb/TASK-1201
2f1c2d4 
TASK-1201 - Use dataRelease from Cellbase in OpenCGA
@juanfeSanahuja
Merge pull request #2225 from opencb/TASK-2390
602632c 
TASK-2390
@jtarraga
Merge pull request #2217 from opencb/TASK-2274
f99edea 
TASK-2274 HRDetect analysis for mutational signatures
@imedina
JUnit minor fixes
bc82ec4
@jtarraga
Resolve conflicts after merging develop, #TASK-2303
3621810
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@jtarraga @juanfeSanahuja @pfurio @imedina @j-coll