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Release/v2.2.0#36

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ALuesink merged 83 commits intomainUMCUGenetics/CustomModules:mainfrom release/v2.2.0UMCUGenetics/CustomModules:release/v2.2.0Copy head branch name to clipboardJun 18, 2024

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Commits

Commits on Jun 30, 2023

• added functionality for AssignToBins

  mraves2

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• added functionality for GenerateBreaks

  mraves2

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• reference to old file added

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• added functionality for MakeInit file

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Commits on Aug 11, 2023

• added new files

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• added ThermoRawFileParser.nf to CustomModules

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Commits on Aug 14, 2023

• added file for listing of raw files

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Commits on Aug 21, 2023

• new files added, existing files modified

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Commits on Aug 25, 2023

• code cleaned up

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• added functionality

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Commits on Sep 1, 2023

• modified files for Nextflow

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• extra files for Nextflow pipeline

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Commits on Oct 20, 2023

• modified files and added new files

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Commits on Dec 21, 2023

• first working version of full NF pipeline

  mraves2

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Commits on Jan 15, 2024

• added parameter for measurements with high m/z

  mraves2

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• added modification of threshold in case of high m/z

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Commits on Feb 20, 2024

• Add EditSummaryFileHappy

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• refactor script in EditSummaryFileHappy

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• add joined column of truth and query samples

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• add delim

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• change column to Type and Filter

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• use meta.id as tag

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• add stageAs to CheckQC

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• typo

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• used lintr and styler to clean up code

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Commits on Feb 21, 2024

• convert qc_value to float

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• change input to qc settings metrics

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• Add docstrings checkqc

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• Split awk and rename output

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• Only add .* if string is provided

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Commits on Feb 22, 2024

• fixed output for TIC plots

  mraves2

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Commits on Feb 26, 2024

• fixed code after cleaning with lintr

  mraves2

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• Merge branch 'feature/DIMS' of github.com:UMCUGenetics/CustomModules into feature/DIMS

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Commits on Feb 29, 2024

• corrections after code clean-up with lintr

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Commits on Mar 26, 2024

• rename output checkqc

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• add versions yaml to VersionLog

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• escape $

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• escape $

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• add git dir to describe

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Commits on Mar 27, 2024

• code review suggestions applied

  mraves2

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  e7eabb3

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• cleaned up AddOnFunctions

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• cleaned up AddOnFunctions

  mraves2

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Commits on Apr 5, 2024

• cleaned up version of fitGaussian.R

  mraves2

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Commits on Apr 8, 2024

• Add changes v2.7

  ALuesink

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• Added helix output file

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Commits on Apr 11, 2024

• Added output_helix.R

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Commits on Apr 12, 2024

• flake8 changes

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• Merge dev

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• Added package for Helix output

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Commits on Apr 15, 2024

• Docstrings summary to newline and comments with uppercase

  ellendejong

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• Change isalpha to punctuation check to determine if filename string or regex

  ellendejong

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• Moved comments to new lines and resolved flake8 errors

  ellendejong

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• Single newline at end of file (.nf)

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• replace noqa W605 with a regex string (r"")

  ellendejong

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• get quotechar from qc settings or use default.

  ellendejong

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• Merge pull request #28 from UMCUGenetics/release/v2.1.0

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• add comment floats to string conversion

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• merge dev.

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• Merge pull request #21 from UMCUGenetics/feature/giabeval

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Commits on Apr 16, 2024

• Cleaned up GenerateViolinPlots AddOnFunctions

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Commits on Apr 18, 2024

• Output paths added

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• Changed to Unidentified steps to parallel

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Commits on Apr 19, 2024

• Added changes HPC and parallelisation Unidentified

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• Added loading package

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• Changed output

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Commits on Apr 22, 2024

• cleaned up peak finding, fill missing functions

  mraves2

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Commits on Apr 26, 2024

• TIC plots and TRFP flag

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• Fix TIC plot pdf

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Commits on May 24, 2024

• corrected error in aggregate lines

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• code review changes applied

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• code review changes applied

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Commits on May 27, 2024

• fixed names of Utils function calls

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Commits on May 30, 2024

• Added Zscore if statement

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• Fixed missing negative HMDB part

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Commits on May 31, 2024

• code review changes applied

  mraves2

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• code review changes applied

  mraves2

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Commits on Jun 4, 2024

• Changes for using Utils

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Commits on Jun 11, 2024

• Merge pull request #32 from UMCUGenetics/feature/update_flask_tools

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Commits on Jun 18, 2024

• Merge pull request #34 from UMCUGenetics/hotfix/v2.1.2

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• Revert "Feature/giabeval"

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• Merge pull request #35 from UMCUGenetics/revert-21-feature/giabeval

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• Merge pull request #22 from UMCUGenetics/feature/DIMS

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• Merge branch 'develop' into release/v2.2.0

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