Code

Release 2.6.0#325

Code

Merged

jonasscheid merged 154 commits intomasternf-core/mhcquant:masterfrom devnf-core/mhcquant:devCopy head branch name to clipboardJun 17, 2024

+5,872-6,726

Commits

Commits on Sep 6, 2023

• Fixed a/c/x/z ion parameter

  steffenlem

  committed
  90d8ccf

Commits on Nov 12, 2023

• wip ms2rescore

  jonasscheid

  committed
  ca415cb

Commits on Nov 29, 2023

• Add ms2rescore module, remove ms2pip and deeplc modules

  jonasscheid

  committed
  2420fa6

• update docs

  jonasscheid

  committed
  1cd26e0

• lint

  jonasscheid

  committed
  66b2bb7

• update citations

  jonasscheid

  committed
  a02885a

Commits on Nov 30, 2023

• bump to dev version

  jonasscheid

  committed
  6abfde0

• remove test_full from gh workflow

  jonasscheid

  committed
  37ee492

• depricate ms2pip and deeplc cli

  jonasscheid

  committed
  d2d2cb0

• fix linting

  jonasscheid

  committed
  c9b5b0b

• remove deeplc and ms2pip imports

  jonasscheid

  committed
  8f07352

• go back to actions/checkout@v2

  jonasscheid

  committed
  9f2c4d3

• correct indentation

  jonasscheid

  committed
  cc29584

Commits on Dec 2, 2023

• rename cli argument in ms2rescore

  jonasscheid

  committed
  b0d2009

Commits on Dec 6, 2023

• filter out not supported peptidehits

  jonasscheid

  committed
  ffdf5a1

Commits on Dec 7, 2023

• bump ms2rescore version to official release

  jonasscheid

  committed
  e9a7527

Commits on Dec 18, 2023

• Merge pull request #293 from jonasscheid/add_ms2rescore

  Show description for d00d9b5
  jonasscheid

  authored
  d00d9b5

Commits on Dec 19, 2023

• Template update for nf-core/tools version 2.11

  nf-core-bot

  committed
  1decec3

Commits on Dec 20, 2023

• Template update for nf-core/tools version 2.11.1

  nf-core-bot

  committed
  ed71e89

Commits on Jan 3, 2024

• expose deeplc calibration set size param

  jonasscheid

  committed
  dc3403b

• test multiple fixed and variable mods

  jonasscheid

  committed
  848ac8a

• fix multiple decoy db generation if only one is given

  jonasscheid

  committed
  1c092c4

• merge template update

  jonasscheid

  committed
  76c40e7

• fix doi in nextflow.config

  jonasscheid

  committed
  d42daa6

• bump module versions

  jonasscheid

  committed
  99a9555

• prettier

  jonasscheid

  committed
  8662ea5

• Update docs/usage.md

  Show description for 00dd0b2
  

  jonasscheid

  and

  mapo9

  authored
  00dd0b2

• Update README.md

  jonasscheid

  authored
  be7396f

Commits on Jan 4, 2024

• change docker runOptions: ms2rescore container has no non-root home directoy

  jonasscheid

  committed
  97a6258

• Merge branch 'merge-template-updates' of https://github.com/jonasscheid/mhcquant into merge-template-updates

  jonasscheid

  committed
  4cc41a3

• prettier

  jonasscheid

  committed
  0d00b14

• Merge pull request #300 from jonasscheid/merge-template-updates

  Show description for 35b0240
  jonasscheid

  authored
  35b0240

• Merge branch 'dev' into test_multiple_mods

  jonasscheid

  committed
  3299531

• Merge branch 'dev' into add_ms2rescore

  jonasscheid

  committed
  62be052

• Merge branch 'dev' into fix_decoydatabase_creation

  jonasscheid

  committed
  b8db4a3

• black formatting

  jonasscheid

  committed
  8252e53

• unpack kwargs

  jonasscheid

  committed
  90409ac

• Merge pull request #299 from jonasscheid/fix_decoydatabase_creation

  Show description for 7eb286f
  jonasscheid

  authored
  7eb286f

• Merge pull request #298 from jonasscheid/test_multiple_mods

  Show description for 1fc7268
  jonasscheid

  authored
  1fc7268

• Merge pull request #297 from jonasscheid/add_ms2rescore

  Show description for 992ac4f
  jonasscheid

  authored
  992ac4f

Commits on Jan 5, 2024

• Merge branch 'nf-core:dev' into dev

  steffenlem

  authored
  1073a86

• Removed mzml renaming after file filter step

  steffenlem

  committed
  85b3463

• temporarily disable neoepitopeprediction due to outdated vcf parsing

  jonasscheid

  committed
  ffbb623

• remove not needed ifEmpty(null) from versions channel

  jonasscheid

  committed
  4dca345

• use nf-core decoydatabase, remove local

  jonasscheid

  committed
  3c8ff6b

• remove not used fdr module

  jonasscheid

  committed
  85c61ce

• use nf-core peakpickerhires, remove local

  jonasscheid

  committed
  f0629fe

• Added ion parameters to ion_annotator test

  

  Cloud User

  committed
  aea21d6

• add nfcore idmerger module, remove local

  jonasscheid

  committed
  ccca493

• update module patj

  jonasscheid

  committed
  460c8c0

• Use nf-core idfilter module, remove local

  jonasscheid

  committed
  2136617

Commits on Jan 6, 2024

• Merge pull request #301 from steffenlem/dev

  Show description for dc6c130
  jonasscheid

  authored
  dc6c130

• delete custom idfilter script

  jonasscheid

  committed
  3af6c1b

• delete pyopenms idfilter module

  jonasscheid

  committed
  d4972ca

Commits on Jan 8, 2024

• replace pyopenms idfilter with nf-core openms module

  jonasscheid

  committed
  27c696f

Commits on Jan 9, 2024

• add idscoreswitcher nf-core module

  jonasscheid

  committed
  8f1a411

Commits on Jan 12, 2024

• add nf-core module idripper, remove local

  jonasscheid

  committed
  e37e9d6

• introduce spectra meta key for easier merge and splitting, adjust quant subworkflow accordingly

  jonasscheid

  committed
  2719b61

Commits on Jan 23, 2024

• change to docker process.containerOptions, fix percolator test profile

  jonasscheid

  committed
  f30c2b6

• add flags that have been set by userEmulation previously

  jonasscheid

  committed
  065e324

• pin prettier version to pass linting

  jonasscheid

  committed
  9bc32e3

Commits on Jan 29, 2024

• try former userEmulation settings in docker.runOptions

  jonasscheid

  committed
  0af6d95

• Template update for nf-core/tools version 2.12

  nf-core-bot

  committed
  fab5530

• Revisit attempt via process.containerOptions

  jonasscheid

  committed
  5067217

Commits on Jan 30, 2024

• merge template

  jonasscheid

  committed
  1c24f24

• [automated] Fix linting with Prettier

  nf-core-bot

  committed
  394a082

Commits on Jan 31, 2024

• update changelog and schema defaults

  jonasscheid

  committed
  b6545ae

• Merge branch 'merging-template-updates' of https://github.com/jonasscheid/mhcquant into merging-template-updates

  jonasscheid

  committed
  6b3b866

• sneak in fix typo

  jonasscheid

  committed
  558049d

• fix lint

  jonasscheid

  committed
  b4dc184

• Merge pull request #304 from jonasscheid/merging-template-updates

  Show description for 840d4d7
  jonasscheid

  authored
  840d4d7

Commits on Feb 16, 2024

• fix typo

  jonasscheid

  committed
  447bba5

• merge dev into feature branch

  jonasscheid

  committed
  f34ebc7

Commits on Feb 19, 2024

• Merge pull request #302 from jonasscheid/fix-docker-permissions

  Show description for b9b2f2a
  jonasscheid

  authored
  b9b2f2a

Commits on Feb 20, 2024

• Template update for nf-core/tools version 2.13

  nf-core-bot

  committed
  4a07016

Commits on Feb 23, 2024

• replace local with nf-core modules and adjust downstream channel handling

  jonasscheid

  committed
  7138ff9

• switch thermorawfileparser from local to nf-core module

  jonasscheid

  committed
  49a5bb6

• move thermorawfileparser config to nf-core section

  jonasscheid

  committed
  5e54eb6

Commits on Feb 24, 2024

• remove channel view

  Show description for 200865a
  

  jonasscheid

  and

  FriederikeHanssen

  authored
  200865a

Commits on Feb 26, 2024

• update changelog and readme

  jonasscheid

  committed
  e52085d

• Merge branch 'dev' into refactor-for-release-2_6

  jonasscheid

  authored
  e7a1938

Commits on Feb 27, 2024

• Merge pull request #310 from jonasscheid/refactor-for-release-2_6

  Show description for ce6ed23
  jonasscheid

  authored
  ce6ed23

Commits on Feb 28, 2024

• merge template

  jonasscheid

  committed
  c04efcf

• move allele input check to utils subworkflow

  jonasscheid

  committed
  9247737

• reinstall idfilter module to fix linting

  jonasscheid

  committed
  364da01

• fix warnings

  jonasscheid

  committed
  ae24f10

Commits on Feb 29, 2024

• Update .github/workflows/awsfulltest.yml

  Show description for 90f617f
  

  jonasscheid

  and

  mashehu

  authored
  90f617f

• Update .github/workflows/awstest.yml

  Show description for 982c268
  

  jonasscheid

  and

  mashehu

  authored
  982c268

• Update nextflow.config

  Show description for 099598f
  

  jonasscheid

  and

  mashehu

  authored
  099598f

• Update subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf

  Show description for ab11c57
  

  jonasscheid

  and

  mashehu

  authored
  ab11c57

• Merge pull request #311 from jonasscheid/merge-template

  Show description for 6966dd9
  jonasscheid

  authored
  6966dd9

• Template update for nf-core/tools version 2.13.1

  nf-core-bot

  committed
  d0a6648

Commits on Mar 1, 2024

• merge template

  jonasscheid

  committed
  20e7994

• Add to changelog

  jonasscheid

  committed
  b259656

• fix typo in changelog

  jonasscheid

  committed
  249af92

• Merge pull request #313 from jonasscheid/merge-template

  Show description for 4351841
  jonasscheid

  authored
  4351841

Commits on Mar 4, 2024

• Fix ms2rescore containerOptions for singulartiy profile

  jonasscheid

  committed
  fa851cf

• Merge pull request #314 from jonasscheid/fix-containerOptions-singularity

  Show description for daa4826
  jonasscheid

  authored
  daa4826

Commits on Mar 8, 2024

• bump ms2rescore container

  jonasscheid

  committed
  069d0c0

• try docker runoptions again

  jonasscheid

  committed
  1777864

Commits on Mar 11, 2024

• bump container build, previous had dependency issues

  jonasscheid

  committed
  5b784e0

• Merge branch 'bump-ms2rescore-container' of https://github.com/jonasscheid/mhcquant into bump-ms2rescore-container

  jonasscheid

  committed
  3811751

• switch to container option

  jonasscheid

  committed
  142fb98

Commits on Mar 12, 2024

• Merge pull request #315 from jonasscheid/bump-ms2rescore-container

  Show description for fec2a66
  jonasscheid

  authored
  fec2a66

Commits on Mar 26, 2024

• Fix validation for bruker files

  jonasscheid

  committed
  1261417

• Merge pull request #316 from jonasscheid/dev

  Show description for e0f2cee
  jonasscheid

  authored
  e0f2cee

Commits on May 8, 2024

• Template update for nf-core/tools version 2.14.0

  nf-core-bot

  committed
  54bdefe

Commits on May 9, 2024

• Template update for nf-core/tools version 2.14.1

  nf-core-bot

  committed
  6d55575

Commits on May 10, 2024

• Merge template updates

  jonasscheid

  committed
  8ee82b1

• fix nf-core lint

  jonasscheid

  committed
  27ee18d

• increment changelog

  jonasscheid

  committed
  ef44bdd

• Merge pull request #320 from jonasscheid/merging-template-updates

  Show description for 7e2f5c3
  jonasscheid

  authored
  7e2f5c3

Commits on May 12, 2024

• remove erroneus subworkflows predict_class1/2 and refine_fdr and corresponding modules and scripts

  jonasscheid

  committed
  003228e

• fix prettier

  jonasscheid

  committed
  e3ed533

• remove legacy klammer param

  jonasscheid

  committed
  45fa1d5

• update docs

  jonasscheid

  committed
  3fc5faa

• update license

  jonasscheid

  committed
  619210c

• delete duplicated local module

  jonasscheid

  committed
  bb9ff54

• adding ms2pip model cache dir option

  jonasscheid

  committed
  ccd0c70

• adjust param description

  jonasscheid

  committed
  465c903

Commits on May 13, 2024

• Merge pull request #321 from jonasscheid/remove_erroneus_hla_prediction

  Show description for 4a4f835
  jonasscheid

  authored
  4a4f835

• Merge branch 'dev' into ms2pip_cachedir

  jonasscheid

  authored
  57fbc3c

• fix lint

  jonasscheid

  committed
  3dd15c0

Commits on May 14, 2024

• Add timstof tests and archive support

  jonasscheid

  committed
  40cf7e5

• update test config paths

  jonasscheid

  committed
  0deda22

• update readme

  jonasscheid

  committed
  1621875

Commits on May 15, 2024

• fix prettier

  jonasscheid

  committed
  b8de2b0

• switch from tab to space tabbing

  jonasscheid

  committed
  11c1f19

• alter ci to run test_timstof and test_full only on push against main

  jonasscheid

  committed
  65980b1

• create third workflow only running on push against main

  jonasscheid

  committed
  95cc7e0

Commits on May 28, 2024

• update docs

  jonasscheid

  committed
  70844e8

• remove full test from ci again, not enough ressources on GH

  jonasscheid

  committed
  99c4201

• rename --skip_quantification to --quantify and set ID mode to default

  jonasscheid

  committed
  16f3e87

• fix prettier

  jonasscheid

  committed
  3caf8c7

• update subway plot

  jonasscheid

  committed
  b4ac8cb

• set all extentions to lower case for simple extention detection

  jonasscheid

  committed
  586d473

• rename timstof tests

  jonasscheid

  committed
  7a6e0f6

• Merge pull request #322 from jonasscheid/ms2pip_cachedir

  Show description for 2b22ec7
  jonasscheid

  authored
  2b22ec7

• Merge branch 'dev' into compression_support

  jonasscheid

  authored
  528e77f

Commits on May 29, 2024

• Merge pull request #323 from jonasscheid/compression_support

  Show description for 0fd0045
  jonasscheid

  authored
  0fd0045

• Update README.md

  Show description for 6d84cc2
  

  jonasscheid

  and

  mapo9

  authored
  6d84cc2

• Update README.md

  Show description for c44687f
  

  jonasscheid

  and

  mapo9

  authored
  c44687f

• Update README.md

  Show description for 5443539
  

  jonasscheid

  and

  mapo9

  authored
  5443539

• Update docs/usage.md

  Show description for 90a953b
  

  jonasscheid

  and

  mapo9

  authored
  90a953b

• Merge branch 'dev' into update_docs

  jonasscheid

  authored
  c9ca5cc

Commits on May 30, 2024

• Merge pull request #324 from jonasscheid/update_docs

  Show description for 5cbc1f7
  jonasscheid

  authored
  5cbc1f7

Commits on May 31, 2024

• fix whitespace

  jonasscheid

  committed
  065ef8a

• add stub to ms2rescore

  jonasscheid

  committed
  9f24ec0

Commits on Jun 15, 2024

• update openms modules

  jonasscheid

  committed
  fd36063

• incorporate suggestions

  jonasscheid

  committed
  a5780a2

• update doc

  jonasscheid

  committed
  2b8af24

• update lint ignore and pipeline version

  jonasscheid

  committed
  0611d30

Commits on Jun 17, 2024

• remove not needed params in stubs, update changelog

  jonasscheid

  committed
  5bfb1d9

• Merge pull request #326 from jonasscheid/prepare-release-2-6-0

  Show description for 722343b
  jonasscheid

  authored
  722343b