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Release 2.5.0 #284

Merged
merged 147 commits into from
Oct 10, 2023
Merged

Release 2.5.0 #284

merged 147 commits into from
Oct 10, 2023

Commits on Apr 28, 2023

  1. Template update for nf-core/tools version 2.8

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    nf-core-bot committed Apr 28, 2023
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Commits on May 15, 2023

  1. Resolve conflicts

    @jonasscheid
    jonasscheid committed May 15, 2023
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  2. resolve more conflicts

    @jonasscheid
    jonasscheid committed May 15, 2023
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  3. fix linting

    @jonasscheid
    jonasscheid committed May 15, 2023
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  4. Merge pull request #264 from nf-core/nf-core-template-merge-2.8 

    Important! Template update for nf-core/tools v2.8
    @jonasscheid
    jonasscheid authored May 15, 2023
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Commits on May 19, 2023

  1. update openms version, rename parser

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    jonasscheid committed May 19, 2023
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Commits on May 26, 2023

  1. add skip_quantification to small test datase

    @jonasscheid
    jonasscheid committed May 26, 2023
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  2. adjust changelog

    @jonasscheid
    jonasscheid committed May 26, 2023
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Commits on May 28, 2023

  1. Merge pull request #266 from jonasscheid/dev 

    Update openms version
    @jonasscheid
    jonasscheid authored May 28, 2023
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Commits on May 30, 2023

  1. Add bruker converter tdf2mzml

    @jonasscheid
    jonasscheid committed May 30, 2023
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  2. fix linting

    @jonasscheid
    jonasscheid committed May 30, 2023
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Commits on May 31, 2023

  1. Merge pull request #267 from jonasscheid/dev 

    Add bruker file converter tdf2mzml
    @jonasscheid
    jonasscheid authored May 31, 2023
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Commits on Jun 2, 2023

  1. fix rawfileparser output bug

    @jonasscheid
    jonasscheid committed Jun 2, 2023
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Commits on Jun 5, 2023

  1. Merge pull request #268 from jonasscheid/dev 

    fix rawfileparser output bug
    @jonasscheid
    jonasscheid authored Jun 5, 2023
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Commits on Jun 20, 2023

  1. Added DeepLC script

    Steffen Lemke committed Jun 20, 2023
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  2. Call deeplc after comet

    Steffen Lemke committed Jun 20, 2023
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  3. Changed input variable of DeepLC

    Steffen Lemke committed Jun 20, 2023
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  4. Added shebang to deeplc script

    Steffen Lemke committed Jun 20, 2023
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  5. Adjusted paramter names for deeplc script

    Steffen Lemke committed Jun 20, 2023
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  6. Fixed parameter name in deeplc script

    Steffen Lemke committed Jun 20, 2023
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  7. Fix input/output parameter names

    Steffen Lemke committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. Added default error calculation

    Steffen Lemke committed Jun 21, 2023
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  2. Added deeplc features to percolator

    Steffen Lemke committed Jun 21, 2023
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  3. Fixed deeplc output

    Steffen Lemke committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Updated schema with DeepLC parameters

    Steffen Lemke committed Jun 22, 2023
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  2. Updated changelog

    Steffen Lemke committed Jun 22, 2023
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  3. Linting

    Steffen Lemke committed Jun 22, 2023
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  4. Fixed linting changes

    Steffen Lemke committed Jun 22, 2023
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  5. Added newline at EOF

    Steffen Lemke committed Jun 22, 2023
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  6. Fixed mail template

    Steffen Lemke committed Jun 22, 2023
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  7. Python black

    Steffen Lemke committed Jun 22, 2023
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  8. Renamed channel comet out

    Steffen Lemke committed Jun 22, 2023
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  9. Fixed input channel for comet

    Steffen Lemke committed Jun 22, 2023
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  10. Added handling of non canonical amino acids for DeepLC module

    Steffen Lemke committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. Added support for noncanonical peptides

    Steffen Lemke committed Jun 23, 2023
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  2. Merge pull request #269 from steffenlem/deeplc 

    Added Deeplc
    @jonasscheid
    jonasscheid authored Jun 23, 2023
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  3. Added MS2pip

    Steffen Lemke committed Jun 23, 2023
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  4. lint

    Steffen Lemke committed Jun 23, 2023
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Commits on Jun 24, 2023

  1. Ran Prettier

    Steffen Lemke committed Jun 24, 2023
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  2. Merge pull request #270 from steffenlem/ms2pip

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    jonasscheid authored Jun 24, 2023
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Commits on Jun 27, 2023

  1. Add filefilter to clean mzml before search

    @jonasscheid
    jonasscheid committed Jun 27, 2023
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  2. add changes to changelog

    @jonasscheid
    jonasscheid committed Jun 27, 2023
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  3. update version

    @jonasscheid
    jonasscheid committed Jun 27, 2023
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  4. Merge pull request #271 from jonasscheid/filefilter 

    Add Filefilter after rawfile parsing
    @steffenlem
    steffenlem authored Jun 27, 2023
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Commits on Jun 29, 2023

  1. Added case insensitive check for file extension

    Steffen Lemke committed Jun 29, 2023
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  2. Added option for default comet parameters file

    Steffen Lemke committed Jun 29, 2023
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  3. Update changelog

    Steffen Lemke committed Jun 29, 2023
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  4. Merge pull request #272 from steffenlem/dev

    @steffenlem
    steffenlem authored Jun 29, 2023
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  5. Optimize resource allocations

    @jonasscheid
    jonasscheid committed Jun 29, 2023
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  6. add changelog

    @jonasscheid
    jonasscheid committed Jun 29, 2023
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  7. typo

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    jonasscheid committed Jun 29, 2023
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  8. Merge branch 'dev' into dev

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    jonasscheid authored Jun 29, 2023
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  9. Merge pull request #273 from jonasscheid/dev 

    Optimize resource allocations
    @steffenlem
    steffenlem authored Jun 29, 2023
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Commits on Jun 30, 2023

  1. Template update for nf-core/tools version 2.9

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    nf-core-bot committed Jun 30, 2023
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Commits on Jul 11, 2023

  1. Fixed extra flag for ms2pip

    Steffen Lemke committed Jul 11, 2023
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Commits on Jul 12, 2023

  1. debug template update

    Jonas Scheid committed Jul 12, 2023
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Commits on Jul 19, 2023

  1. add loading modules.conf again

    Jonas Scheid committed Jul 19, 2023
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  2. changelog

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  3. fix nextflow version for fulltest

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  4. fix gh ci for fulltest

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  5. add novel params to fulltest

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  6. fix old conda implementation in modules

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  7. adjust authors

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  8. remove fastqc from citations

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  9. prettier

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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  10. adjust license

    @jonasscheid
    jonasscheid committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. Update nextflow.config

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    jonasscheid authored Jul 20, 2023
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  2. Merge pull request #274 from nf-core/nf-core-template-merge-2.9 

    Important! Template update for nf-core/tools v2.9
    @jonasscheid
    jonasscheid authored Jul 20, 2023
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Commits on Jul 27, 2023

  1. Merge remote-tracking branch 'upstream/dev' into dev

    Steffen Lemke committed Jul 27, 2023
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Commits on Aug 18, 2023

  1. Fixed parameter calling in psmfeatureextractor

    @steffenlem
    steffenlem committed Aug 18, 2023
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  2. Merge pull request #275 from steffenlem/dev 

    Fixed extra flag setting for ms2pip
    @jonasscheid
    jonasscheid authored Aug 18, 2023
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  3. refactor naming

    @jonasscheid
    jonasscheid committed Aug 18, 2023
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  4. more naming changes

    @jonasscheid
    jonasscheid committed Aug 18, 2023
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  5. more namings

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    jonasscheid committed Aug 18, 2023
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  6. Restructure quant part 1

    @jonasscheid
    jonasscheid committed Aug 18, 2023
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  7. Add post-alignment merger for featurefinder

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    jonasscheid committed Aug 18, 2023
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Commits on Aug 28, 2023

  1. ensure percolator tdc

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    jonasscheid committed Aug 28, 2023
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  2. Merge branch 'dev' of https://github.com/jonasscheid/mhcquant into dev

    @jonasscheid
    jonasscheid committed Aug 28, 2023
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Commits on Aug 30, 2023

  1. Merge pull request #279 from jonasscheid/dev 

    Ensure Percolator target decoy competition
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    jonasscheid authored Aug 30, 2023
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Commits on Sep 4, 2023

  1. adjust such that quant_fdr can be used

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Commits on Sep 17, 2023

  1. restructure quant such that map alignment comes after percolator

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    jonasscheid committed Sep 17, 2023
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Commits on Sep 18, 2023

  1. Update to openms 3.0.0

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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  2. replace dev container with mulled container on quay

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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  3. Depricate old rt prediction

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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  4. depricate openms rt prediction

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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  5. depricate openms rt prediction

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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  6. remove fastq image in docs

    @jonasscheid
    jonasscheid committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. adjust ffid settings

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    jonasscheid committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Update publishing files

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  2. Add scoreswitcher for quant and optional filefilter

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  3. cosmetics

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  4. Adjust publihsed files

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  5. filefilter optional in schema

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  6. updated docs

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  7. bump version

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  8. bump openms conda version

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  9. linting

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  10. merge dev into feature branch, fix conflict

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  11. update changelog

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  12. remove fastqc

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  13. fix typo

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  14. update citations

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  15. fix lint

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  16. fix typo

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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  17. fix citation

    @jonasscheid
    jonasscheid committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. fix wrong channel elements in ionannotator and cleanup

    @jonasscheid
    jonasscheid committed Sep 21, 2023
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  2. fix ionannotator input for mzml files

    @jonasscheid
    jonasscheid committed Sep 21, 2023
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Commits on Sep 25, 2023

  1. Template update for nf-core/tools version 2.10

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    nf-core-bot committed Sep 25, 2023
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Commits on Sep 27, 2023

  1. harmonize exporter modules between id and quant

    @jonasscheid
    jonasscheid committed Sep 27, 2023
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  2. add requested comment

    @jonasscheid
    jonasscheid committed Sep 27, 2023
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  3. cosmetics

    @jonasscheid
    jonasscheid committed Sep 27, 2023
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  4. adjust filenaming in maptransformer

    @jonasscheid
    jonasscheid committed Sep 27, 2023
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Commits on Sep 28, 2023

  1. Refactor grouping

    @jonasscheid
    jonasscheid committed Sep 28, 2023
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  2. Encapsulate quant in subworkflow

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    jonasscheid committed Sep 28, 2023
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  3. Add test profi

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    jonasscheid committed Sep 28, 2023
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  4. prettier

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    jonasscheid committed Sep 28, 2023
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  5. adjust ci

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    jonasscheid committed Sep 28, 2023
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  6. add test profiles to nextflow.config

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    jonasscheid committed Sep 28, 2023
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  7. styling

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    jonasscheid committed Sep 28, 2023
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  8. add ionannotator test

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    jonasscheid committed Sep 28, 2023
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Commits on Oct 2, 2023

  1. merge template updaet

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    jonasscheid committed Oct 2, 2023
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  2. addd subwayplot

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    jonasscheid committed Oct 2, 2023
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  3. update changelog

    @jonasscheid
    jonasscheid committed Oct 2, 2023
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  4. fix nfcore linting

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    jonasscheid committed Oct 2, 2023
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  5. set white background of subway plot

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    jonasscheid committed Oct 2, 2023
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  6. limit mem for ci

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    jonasscheid committed Oct 2, 2023
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  7. limit cpus for ci

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    jonasscheid committed Oct 2, 2023
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Commits on Oct 3, 2023

  1. spectrum batch size limit on ci tests to prevent crashing workflows

    @jonasscheid
    jonasscheid committed Oct 3, 2023
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  2. Update pyopenms to latest version in ionannotator

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    jonasscheid committed Oct 3, 2023
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  3. increase speed of ci test

    @jonasscheid
    jonasscheid committed Oct 3, 2023
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  4. typo

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    jonasscheid committed Oct 3, 2023
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  5. remove unused dependency

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    jonasscheid committed Oct 3, 2023
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  6. speed up ci quant and fulltest

    @jonasscheid
    jonasscheid committed Oct 3, 2023
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  7. Add comments to subworkflows

    @jonasscheid
    jonasscheid committed Oct 3, 2023
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  8. update changelog

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    jonasscheid committed Oct 3, 2023
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  9. Merge pull request #280 from jonasscheid/rearrange_quant

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    jonasscheid authored Oct 3, 2023
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Commits on Oct 7, 2023

  1. incorporate feedback

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    jonasscheid committed Oct 7, 2023
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Commits on Oct 8, 2023

  1. Movve quant test to test full bc of github limitations

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    jonasscheid committed Oct 8, 2023
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  2. move quant test solely to test_full

    @jonasscheid
    jonasscheid committed Oct 8, 2023
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  3. update warning for refine fdr

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    jonasscheid committed Oct 8, 2023
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  4. prettier

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    jonasscheid committed Oct 8, 2023
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  5. remove deeplc and ms2pip from test_full since test stops bc of runtime

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    jonasscheid committed Oct 8, 2023
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  6. reduce test_full bc no more storage of device (github)

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    jonasscheid committed Oct 8, 2023
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  7. remove class1 and class2 from test_full

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    jonasscheid committed Oct 8, 2023
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  8. only use quant in test_full due to space issue on gh

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    jonasscheid committed Oct 8, 2023
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Commits on Oct 9, 2023

  1. feedback

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    jonasscheid committed Oct 9, 2023
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  2. Merge pull request #285 from jonasscheid/rearrange_quant 

    Final changes for release 2.5.0
    @jonasscheid
    jonasscheid authored Oct 9, 2023
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