1.7.0 - Caracas

What's Changed

• Increase dev version by @ypriverol in #579
• fixing of bug in msstats_tmt.R (Issue: Error in the msstats_tmt.R function parse_contrasts #577) by @kai-lawsonmcdowall in #578
• Pass correct flag to ProteinQuantifier by @johnne in #581
• fixed rescoring range bugs by @daichengxin in #583
• update pmultiqc version 0.0.36 by @ypriverol in #595
• Support ppm fragment tolerance via alphapeptdeep feature generator by @Copilot in #597
• minor bug change to pmultiqc by @ypriverol in #598
• 🐛 allow editing using nf-core pipelines schema build by setting fa_icon by @enryH in #590
• 🎨 address ifEmpty(null) by @enryH in #600
• Upgrade trfp 1.3.4 -> 1.4.5 by @ypriverol in #601
• Add support for TMT16 and TMT18 correction matrix files by @MaLLLiYA in #599
• Update and clarify SDRF and Json-Parameter parsing by @enryH in #596
• Reduce logo size used in pmultiqc by @yueqixuan in #605
• More linting by @enryH in #602
• some updates related with diann, ptms and pmultiqc small issues by @ypriverol in #614
• update quantms-utils 0.0.24 & pmultiqc 0.0.39 by @ypriverol in #615
• Fix trailing whitespace and code formatting by @Copilot in #618
• Format by @enryH in #603
• bug fix when parameter model_dir is wrongly provided by @ypriverol in #619
• Error of quantms-rescoring process with AWS by @ypriverol in #621
• Add support for .dia file format and improve file format documentation by @Copilot in #623
• Add onsite module by @weizhongchun in #626
• move thermorawfileparser from local to bigbio nf-core by @daichengxin in #627
• update quantms-rescoring to support MS2 transfer learning by @daichengxin in #629
• fixed quantms-rescoring by @daichengxin in #631
• using the bigbio onsite module by @weizhongchun in #630
• Fix some issues in onsite by @weizhongchun in #634
• small changes for release by @ypriverol in #635
• minor changes for release by @ypriverol in #636
• Minor changes by @ypriverol in #637
• Release 1.7.0 - Major changes with quantms-rescoring by @ypriverol in #625

New Contributors

• @kai-lawsonmcdowall made their first contribution in #578
• @johnne made their first contribution in #581
• @MaLLLiYA made their first contribution in #599
• @weizhongchun made their first contribution in #626

Full Changelog: 1.6.0...1.7.0

1.6.0 - Munich

What's Changed

• increase dev version 1.6.0dev by @ypriverol in #556
• README_links by @enryH in #560
• Template update 3.3.2 of nf-core an other minor updates by @ypriverol in #566
• Small changes remaining from Template 3.3.2 update by @ypriverol in #567
• support pmultiqc 0.0.31 by @yueqixuan in #570
• update quantms-rescoring and support AalphaPeptDeep model by @daichengxin in #571
• minor changes in the rescoring version by @ypriverol in #573
• preparing for quantms release 1.6.0 by @ypriverol in #575
• Release 1.6.0 by @ypriverol in #574

New Contributors

• @yueqixuan made their first contribution in #570

Full Changelog: 1.5.0...1.6.0

1.5.0 - Zürich

What's Changed

• Update for README.md by @imeMFK01 in #531
• preparing for version 1.4.1dev by @ypriverol in #530
• pmultiqc updated 0.0.27 version by @ypriverol in #537
• quantms-utils 0.0.23 & sdrf-pipelines 0.0.32 by @ypriverol in #539
• add mztab to results for pmultiqc by @ypriverol in #541
• pmultiqc version increased to 0.0.28. Error fixed with diann_report.tsv by @ypriverol in #542
• add Fabian Egli as contributor by @fabianegli in #543
• Fixing bug issues with SNR; quantms-utils -> quantms-rescoring by @ypriverol in #544
• small bug in SNR step by @ypriverol in #545
• Minor refinements with quantms code style, update msstats LFQ -> 4.14.0 by @ypriverol in #547
• prepare for release 1.4.1 by @ypriverol in #548
• Standardization of names in meta.yml for all tools & Big refactoring for all modules to subfolders by @ypriverol in #551
• removed features extract and idscoreswitcher by @daichengxin in #554
• Adding met-excision as parameter to DIA and DDA workflows by @ypriverol in #555
• Release with multiple bug fixed 1.5.0 by @ypriverol in #549

New Contributors

• @imeMFK01 made their first contribution in #531

Full Changelog: 1.4.0...1.5.0

1.4.0 - Tübingen

What's Changed

• quantms 0.0.10 -> 0.0.11 by @ypriverol in #419
• fixed msgfdb index memory bug by @daichengxin in #420
• update to openms 3.2.0 by @ypriverol in #423
• Dev by @ypriverol in #426
• update quantms-utils=0.0.12 by @ypriverol in #429
• Revert thermorawfileparser by @daichengxin in #433
• update figure by @daichengxin in #435
• minor changes - remove bib-nodes.config by @ypriverol in #438
• Improving configs for OpenMS dev and DIANN versions over 1.8.1 by @ypriverol in #441
• update confs - dev and pride ebi by @ypriverol in #443
• update container for msgf_plus indexing. by @ypriverol in #444
• changes in pride slurm config by @ypriverol in #445
• update msgf_plus process to remove the process tag by @ypriverol in #446
• minor changes in pride resource limits by @ypriverol in #449
• Remove posterior_probabilities parameter. by @ypriverol in #450
• quanmts-utils 0.0.15 -> 0.0.17: ms2rescore bug solved by @ypriverol in #451
• Support for DIANN 1.9.2, output all files. by @daichengxin in #454
• Optimization of process resources by @ypriverol in #456
• Fixing quantms rescoring bugs by @ypriverol in #462
• major change to run CI on dev using dev conf by @ypriverol in #464
• quantms-rescoring 0.0.3 -> 0.0.4, fix ms2rescore by @ypriverol in #472
• openms release 3.2.0 -> 3.3.0 by @ypriverol in #474
• more help added to MSGF protocol, update template 3.2.0 by @ypriverol in #476
• change the error ms2rescore to the corresponding search engine by @ypriverol in #483
• support for DIA-NN 2.0 by @daichengxin in #485
• Fixed MSGF TMT MS3 by @daichengxin in #486
• quantms-rescoring changed 0.0.5 by @ypriverol in #489
• Update CHANGELOG.md by @daichengxin in #490
• Generation of MS1 features on mzml statistics, quantms-utils 0.0.20 by @ypriverol in #494
• Changes the CI/CD for testing Dev OpenMS in Dev PRs by @ypriverol in #496
• quantms-rescoring 0.0.6 by @ypriverol in #498
• Small bug (issue #499) introduced in the config files fixed by @ypriverol in #500
• add ms2rescore singularity to wave by @ypriverol in #503
• Improving DIA workflow with new parameters, and logs originally from DIANN (original issue #481 comments) by @an-altosian in #495
• Controlling multiple logs in CI/CD by @ypriverol in #508
• avoid silent skipping of ConsensusID by @enryH in #501
• dump parameters of pipeline by @enryH in #502
• update quantms-rescoring 0.0.6 -> 0.0.7 by @ypriverol in #509
• [DO NOT MERGE] Big PR to remove Conda Support by @ypriverol in #515
• Fixed small bug with singularity in OpenMS by @ypriverol in #518
• quantms-rescoring 0.0.9 and cleaning spectra step by @ypriverol in #519
• update name of variable in process by @ypriverol in #520
• Release 1.4.0 version in Bigbio by @ypriverol in #521

New Contributors

• @an-altosian made their first contribution in #495
• @enryH made their first contribution in #501

Full Changelog: 1.3.0...1.4.0

bigbio/quantms v1.3.0 - Santiago de Cuba

What's Changed

• Add new modules by @daichengxin in #1
• Add input subworkflow and thermorawfileparser by @daichengxin in #3
• Add DatabaseSearchEngines Subworkflow by @daichengxin in #14
• Add PSMRescoring、PSMFDRControl、Phosphoscoring、ProteinInference、Featur… by @daichengxin in #18
• docker openms 6.0 -> 2.7pre by @ypriverol in #19
• Add LFQ part and fixed bugs by @daichengxin in #20
• add pmulitqc by @daichengxin in #21
• fixed bug and publish files by @daichengxin in #22
• Improve docs by @ypriverol in #23
• minor changes by @ypriverol in #25
• docs by @ypriverol in #26
• docs by @ypriverol in #27
• docs improvements by @ypriverol in #28
• docs by @ypriverol in #29
• docs by @ypriverol in #30
• docs by @ypriverol in #31
• dcos by @ypriverol in #32
• docs by @ypriverol in #33
• clean docs by @ypriverol in #34
• quantms by @ypriverol in #40
• minor changes by @ypriverol in #41
• improvements by @ypriverol in #42
• improvements conda by @ypriverol in #43
• improvements conda by @ypriverol in #44
• improvements by @ypriverol in #45
• improvements by @ypriverol in #46
• conda improvements by @ypriverol in #47
• improve conda by @ypriverol in #49
• conda by @ypriverol in #50
• update name by @daichengxin in #51
• output msgf and comet idxml file by @daichengxin in #52
• conda increase to 0.0.19 by @ypriverol in #53
• openms-2.7 in bioconda by @ypriverol in #54
• openms in bioconda by @ypriverol in #55
• openms-2.7 in bioconda by @ypriverol in #56
• rollback inference by @ypriverol in #57
• update quantms by @daichengxin in #59
• idmapper changes by @ypriverol in #60
• ebicluster by @ypriverol in #61
• fixed by @ypriverol in #63
• minor change by @ypriverol in #64
• TMT improvements using openms=2.8.0dev by @ypriverol in #67
• Add output files by @daichengxin in #70
• forgot image by @jpfeuffer in #72
• manual merge of the template update 2.2 branch by @jpfeuffer in #73
• version fix by @daichengxin in #78
• remove multiqc by @daichengxin in #82
• add DIA workflow by @daichengxin in #112
• update meta.nf by @daichengxin in #116
• fixed error by @daichengxin in #124
• diann container from ypriverol -> biocontainers by @ypriverol in #118
• Template 2.3 update by @ypriverol in #126
• Utils updated by @ypriverol in #128
• Documentation for nf-core by @ypriverol in #129
• DIA improvement by @daichengxin in #132
• minor changes to improve CI speed by @ypriverol in #133
• increase min_peptide in test by @ypriverol in #134
• minor fix by @daichengxin in #135
• Template updated 2.3.1 by @ypriverol in #139
• Template update 2.3.2 by @jpfeuffer in #142
• updates by @ypriverol in #143
• Major fix by @daichengxin in #145
• pull nf-core and update pmultiqc by @daichengxin in #152
• add DIA triqler and MSstats by @daichengxin in #153
• diann 1.8.1 by @ypriverol in #154
• skip msstats tests in PTM tests by @ypriverol in #155
• Master by @ypriverol in #157
• Enhancement/logging by @daichengxin in #161
• [FIX] AWS and conda by @jpfeuffer in #163
• add MSstatsTMT and update MSstats by @daichengxin in #158
• Tests changed, move them to test-datasets by @ypriverol in #167
• Sync with nf-core by @jpfeuffer in #170
• Sync with nf-core by @jpfeuffer in #174
• refactor DIA-NN step 1 by @daichengxin in #169
• add name of each ID step by @daichengxin in #176
• restruct DIA-NN step2 by @daichengxin in #178
• Restruct DIA-NN step 3,4,5 by @daichengxin in #179
• Diann update by @ypriverol in #182
• Changelog and DIA-NN double-check by @daichengxin in #184
• [Docu] update metro by @jpfeuffer in #185
• [FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. by @jpfeuffer in #187
• enforce style and add aws test by @daichengxin in #186
• minor fixed by @daichengxin in #193
• quick fix by @daichengxin in #195
• rename output by @daichengxin in #200
• add msstats_in by @daichengxin in #204
• Update main.nf by @ypriverol in #203
• fixed by @daichengxin in #207
• update pmultiqc by @daichengxin in #208
• Added the decoys to TMT output by @ypriverol in #210
• enable mzTab for DIA-NN by @WangHong007 in #205
• print warning info when run DIA-NN with conda by @daichengxin in #212
• fix version by @daichengxin in #213
• small fixs by @WangHong007 in #218
• Upgrade 2.5.1 template by @ypriverol in #220
• Tetsrun by @fabianegli in #222
• Code maintenance by @fabianegli in #221
• Update pmultiqc module to 0.0.14 by @ypriverol in #225
• Test pmultiqc v0.0.15 to see if it works by @WangHong007 in #226
• testing with dev version of OpenMS 2.8.0 by @ypriverol in #229
• dynamic version by @WangHong007 in #230
• Fix config warnings by @jpfeuffer in #232
• fixed bugs by @daichengxin in #234
• improve sdrf validation hint by @daichengxin in #237
• enable spectra_ref in mzTab by @WangHong007 in #240
• pmultiqc move from 0.0.17 -> 0.0.18 by @ypriverol in #242
• pmultiqc:0.0.18 -> 0.0.19 by @ypriverol in #249
• Add max_missed_cleavages option to msgf by @jpfeuffer in #245
• add msstats threshold by @daichengxin in #252
• Parallel mzml_statistics by @WangHong007 in #257
• Reduce memory usage in diann_convert by @WangHong007 in #260
• Major update of latest template from nf-core by @ypriverol in #262
• Dev by @ypriverol in #264
• small change. by @ypriverol in #265
• Fixing multiple bugs of sage quantms by @ypriverol in #279
• Dev by @ypriverol in #281
• sdrf-pipelines version 0.0.24 and parameters for msstats tmt by @ypriverol in #284
• update some proce...