Code

Release v2.1.0#26

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melferink merged 100 commits intomainUMCUGenetics/CustomModules:mainfrom release/v2.1.0UMCUGenetics/CustomModules:release/v2.1.0Copy head branch name to clipboardApr 2, 2024

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Commits

Commits on Jul 24, 2023

• Added MosaicHunter to the workflow

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  0036de6

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• Changed the mosaichunter docker url

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• Refactor file name mosaichunter.nf to MosaicHunter.nf

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Commits on Jul 25, 2023

• Refactor of double quoutes to single

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Commits on Jul 26, 2023

• Refactor input declaration for MosaicHunter

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• Added dockerfile

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Commits on Jul 31, 2023

• Refactor of script block to shell block with right variables

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Commits on Aug 1, 2023

• Set the output of MH step two to optional

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Commits on Aug 3, 2023

• Fix for MH second step config file

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• Fix for input of step specific config files

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Commits on Aug 9, 2023

• Added rename functionality of output file to include sampleID

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• Swapped publishDir to process with file rename functionality to add sampleID in output file

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• Refactor of single quotes to double quotes for publishdir

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Commits on Sep 1, 2023

• Refactor removal of accolades for publishdir

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Commits on Oct 26, 2023

• Refactor for output dir with rename of output files MosaicHunter

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Commits on Dec 7, 2023

• Refactor of MosiacHunter process names to include an underscore

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Commits on Dec 13, 2023

• added gendercheck

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• refactor

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• refactor

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• added

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  e0c7b36

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• added

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  d1579af

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• removed

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  962c0ef

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• fix

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  4ce083e

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• included closing bracket

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  a462418

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• flake8 refactor

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Commits on Dec 14, 2023

• refactor + translation

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  344abf6

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• refactor

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  5eed5da

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• fix

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  635722f

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• general update to one process

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  e34186d

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• removed

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• removed

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Commits on Dec 18, 2023

• support for single file input of same QC. changes made by Ellen

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Commits on Jan 17, 2024

• Wrapped individual variables in tuples in val()

  BasMonkey

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Commits on Jan 26, 2024

• Added second config file for MosaicHunter

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Commits on Feb 7, 2024

• refactor

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• added tests

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• permission same as other files

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• refactor

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  3f8c0f9

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• Merge branch 'develop' into feature/gender_checkY

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  531e845

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• refactor

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• chmod

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Commits on Feb 9, 2024

• Merge remote-tracking branch 'origin/develop' into feature/nextflow_upgrade_23_10_0

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Commits on Feb 14, 2024

• Refactor of MosaicHunter process names, tags and labels

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  7528eae

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• Updated comments

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  3e4f629

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• Refactor of process name in the input of MosicHunter Mosaic Variant Calculation process

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Commits on Feb 16, 2024

• Removed config files from CustomModules

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Commits on Feb 19, 2024

• Fixed indents for input and output

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  c85c0d3

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• Removed redundant tag declaration

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• Refactor of process "docstring" comments

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• Refactor of process metadata

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  05d2084

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• Fixed typo

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  e1ea4cb

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Commits on Feb 26, 2024

• refactor

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  be0e2ea

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• renamed

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  4dd1bc0

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• fixed typo

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  170de6a

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• added test. Removed double tests

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  577f69c

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• refactor mark.parametrize

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• refactor

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Commits on Feb 29, 2024

• changed into male/female only based on 1 threshold

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Commits on Mar 5, 2024

• Merge pull request #17 from UMCUGenetics/feature/gender_checkY

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• Merge branch 'develop' into feature/MosaicHunter

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Commits on Mar 8, 2024

• Added gender parsing step to MosaicHunter

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• Restored acidentially removed new line at end of file

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  ecf6ae8

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• Fixed in- and output of gender data

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  3d078c1

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• Added get gender from bam python script to mosaic hunter

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  7fa1bb8

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• Changed baseDir to projectDir

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• Refactor of all baseDir to projectDir

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• Merge remote-tracking branch 'origin/develop' into feature/nextflow_upgrade_23_10_0

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  dbd936b

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• Added forced field to tsv file

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• Added docstrings

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• Added docstring

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  2ba5ba5

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• Refactor of baseDir to projectDir

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• Added dockerfile for gendercheck image

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  0043ee4

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• Refactor of pysamimage to new selfhosted image

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Commits on Mar 11, 2024

• Refactor of write gender data to file method

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• Added unit tests for MosaicHunter get gender data methods

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  9f9f7ec

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• PEP8 refactor

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• refactor due to renaming sample_udf_dx function in clarity_epp

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• renamed to SampleUDFDx

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  86fa5b2

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• Fixed the assertions + params in test

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  c9a0de7

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• Fixed the returns of the get gender

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• Added requirements for python test for MosaicHunter getgender

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Commits on Mar 12, 2024

• Removed redundant comment

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• Indentation Fix

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Commits on Mar 13, 2024

• Refactor of container name

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• Removed redundant comment

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Commits on Mar 15, 2024

• Refactor of single quotes to double quotes

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• Refactor for in and outputs of MH steps

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• Added missing file extension

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Commits on Mar 19, 2024

• Fixed in and outputs

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Commits on Mar 20, 2024

• Added indents for shell script of MosaicHunter

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Commits on Mar 27, 2024

• Merge pull request #20 from UMCUGenetics/feature/MosaicHunter

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• Merge pull request #23 from UMCUGenetics/feature/nextflow_upgrade_23_10_0

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• Merge pull request #25 from UMCUGenetics/develop

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• Merge pull request #24 from UMCUGenetics/feature/gender_checkY

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• Merge pull request #27 from UMCUGenetics/develop

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Commits on Mar 28, 2024

• Removed DSL 2 preview line

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• Added missing val()

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• refactor to include val()

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Commits on Mar 29, 2024

• flake8 changes. Moved comments

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Commits on Apr 2, 2024

• refactor flake8

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