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Release/12.1.0 #2069

Merged
merged 24 commits into from
Mar 5, 2024
Merged

Release/12.1.0 #2069

merged 24 commits into from
Mar 5, 2024

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jemten
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@jemten jemten commented Feb 21, 2024 •
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This PR adds | fixes:

MIP version 12.1.0

  • Adds optional trimming of reads with Fastp for the DNA workflow, turned on by default
  • Adds automatic fail in analaysisrunstatus for cases where the peddy detects errors in the pedigree
  • Adds automatic fail in analaysisrunstatus for cases where the peddy detects a discrepancy between the given and calculated gender

Tools

  • Fastp: 0.23.4

Databases

clinvar: 20231203 -> 20240215
loqusdb snapshot: 20231204 -> 20240220

How to test:

  • Automatic and continuous test suite

Expected outcome:

  • Installation, unit and integration test suite pass

Review:

  • Code review
  • Tests pass

This version is a:

  • MAJOR - when you make incompatible API changes. If applicable record manual test results in PR header
  • MINOR - when you add functionality in a backwards compatible manner. If applicable record manual test results in PR header
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

jemten and others added 23 commits October 9, 2023 10:33
@jemten
Delete 643594-miptest_metrics_deliverables.yaml
e1b66da
@jemten
Merge pull request #2056 from Clinical-Genomics/release/12.0.1
60cdffb 
Release/12.0.1
@jemten
Merge pull request #2061 from Clinical-Genomics/release/12.0.2
1c8e608 
merge release 12.0.2 into develop
@jemten
Merge pull request #2064 from Clinical-Genomics/release/12.0.3
b43dc0f 
Merge release/12.0.3 into dev
@jemten
adding command module
d985223
@jemten
adding fastp analysis recipe
0d3f08f
@jemten
adding fastp to install
7e4fc74
@jemten
adding documentation
29217b0
@jemten
fix fastp version regexp
506e7f4
@jemten
one more regexp fix
381e518
@jemten
fixing fastp thread name
9522f3a
@jemten
adding fastp reports
2ba1e13
@jemten
Merge pull request #2065 from Clinical-Genomics/fastp
20b3d30 
Fastp
@jemten
adds automatic ped_check fail
25881c3
@jemten
loqus and clinvar update
f0e1a93
@jemten
adds sex_check
33107c6
@jemten
update regexp_file
eadb965
@jemten
reverting vep update
797baf1
@jemten
Merge pull request #2067 from Clinical-Genomics/update_clinvar_loqusdb
d6baf44 
loqus and clinvar update
@jemten @peterpru
Update lib/MIP/Qcc_regexp.pm
dc66fad 
Co-authored-by: Peter Pruisscher <[email protected]>
@jemten
Merge pull request #2066 from Clinical-Genomics/peddy_check
010a180 
adds automatic ped_check fail
@jemten
updating to mip v12.1.0
efa4fe0
@jemten
adding new rankmodel to download
1eda07f
@jemten jemten marked this pull request as ready for review February 22, 2024 16:20
henrikstranneheim
henrikstranneheim previously approved these changes Feb 23, 2024
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💪

lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm Outdated Show resolved Hide resolved
@jemten jemten merged commit 073b9e5 into master Mar 5, 2024
9 checks passed
@jemten jemten deleted the release/12.1.0 branch March 5, 2024 08:48
@jemten jemten restored the release/12.1.0 branch March 5, 2024 08:52
@jemten jemten deleted the release/12.1.0 branch March 5, 2024 09:35
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@jemten @henrikstranneheim