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Release v2.1.0 #26

Merged
merged 100 commits into from
Apr 2, 2024
Merged

Release v2.1.0 #26

merged 100 commits into from
Apr 2, 2024

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melferink
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@melferink melferink commented Mar 27, 2024 •
edited by BasMonkey
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BasMonkey and others added 30 commits July 24, 2023 12:37
@BasMonkey
Added MosaicHunter to the workflow
0036de6
@BasMonkey
Changed the mosaichunter docker url
4a6899b
@BasMonkey
Refactor file name mosaichunter.nf to MosaicHunter.nf
d645819
@BasMonkey
Refactor of double quoutes to single
74aa077
@BasMonkey
Refactor input declaration for MosaicHunter
de70e96
@BasMonkey
Added dockerfile
936a09f
@BasMonkey
Refactor of script block to shell block with right variables
f2f4779
@BasMonkey
Set the output of MH step two to optional
63d6502
@BasMonkey
Fix for MH second step config file
7d8cabe
@BasMonkey
Fix for input of step specific config files
1ada9ee
@BasMonkey
Added rename functionality of output file to include sampleID
c6421ae
@BasMonkey
Swapped publishDir to process with file rename functionality to add s…
d95745c 
…ampleID in output file
@BasMonkey
Refactor of single quotes to double quotes for publishdir
72e9c22
@BasMonkey
Refactor removal of accolades for publishdir
a07e74a
@BasMonkey
Refactor for output dir with rename of output files MosaicHunter
0ef5fe1
@BasMonkey
Refactor of MosiacHunter process names to include an underscore
a2da773
@melferink
added gendercheck
226a224
@melferink
refactor
901729d
@melferink
refactor
60e0d19
@melferink
added
e0c7b36
@melferink
added
d1579af
@melferink
removed
962c0ef
@melferink
fix
4ce083e
@melferink
included closing bracket
a462418
@melferink
flake8 refactor
e232dab
@melferink
refactor + translation
344abf6
@melferink
refactor
5eed5da
@melferink
fix
635722f
@melferink
general update to one process
e34186d
@melferink
removed
09b33da
melferink and others added 21 commits March 11, 2024 09:43
@melferink
renamed to SampleUDFDx
86fa5b2
@BasMonkey
Fixed the assertions + params in test
c9a0de7
@BasMonkey
Fixed the returns of the get gender
9570808
@BasMonkey
Added requirements for python test for MosaicHunter getgender
34f53e1
@BasMonkey
Removed redundant comment
bebdfcd
@BasMonkey
Indentation Fix
f82e912
@BasMonkey
Refactor of container name
8af8781
@BasMonkey
Removed redundant comment
5b55ac0
@BasMonkey
Refactor of single quotes to double quotes
09dba80
@BasMonkey
Refactor for in and outputs of MH steps
882d59e
@BasMonkey
Added missing file extension
2290b37
@BasMonkey
Fixed in and outputs
8531d55
@BasMonkey
Added indents for shell script of MosaicHunter
196e5d8
@BasMonkey
Merge pull request #20 from UMCUGenetics/feature/MosaicHunter
d78e272 
Feature/mosaic hunter
@BasMonkey
Merge pull request #23 from UMCUGenetics/feature/nextflow_upgrade_23_…
cc603d1 
…10_0

Feature/nextflow upgrade 23 10 0
@melferink
Merge pull request #25 from UMCUGenetics/develop
227538e 
Develop
@melferink
Merge pull request #24 from UMCUGenetics/feature/gender_checkY
50cb86a 
Refactor sample_udf_dx function
@melferink
Merge pull request #27 from UMCUGenetics/develop
cf3e64f 
Develop
@BasMonkey
Removed DSL 2 preview line
91258ad
@BasMonkey
Added missing val()
c9a7fdb
@melferink
refactor to include val()
dd4391d
ellendejong
ellendejong previously requested changes Mar 29, 2024
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@ellendejong ellendejong left a comment •
edited by rernst
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Most commits have been approved previously.
Except 91258ad, c9a7fdb, dd4391d: OK.

However, not all files are conform flake8 which is required.

ClarityEpp/SampleUDFDx.nf Show resolved Hide resolved
GenderCheck/calculate_gender.py Show resolved Hide resolved
GenderCheck/test_calculate_gender.py Outdated Show resolved Hide resolved
MosaicHunter/1.0.0/Dockerfile Outdated Show resolved Hide resolved
@BasMonkey BasMonkey requested a review from ellendejong March 29, 2024 12:03
@melferink melferink requested a review from rernst April 2, 2024 08:40
rernst
rernst approved these changes Apr 2, 2024
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Comments by @ellendejong are taken care of.

@rernst rernst dismissed ellendejong’s stale review April 2, 2024 08:44

Comments by @ellendejong are taken care of.

@melferink melferink merged commit 5ae3239 into main Apr 2, 2024
@BasMonkey BasMonkey deleted the release/v2.1.0 branch April 15, 2024 07:48
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@BasMonkey BasMonkey BasMonkey left review comments

@rernst rernst rernst approved these changes

@ellendejong ellendejong Awaiting requested review from ellendejong

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4 participants
@melferink @rernst @BasMonkey @ellendejong