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 process to openms dev by @ypriverol in #289
• Dev by @ypriverol in #291
• id transfer threshold update by @ypriverol in #292
• updating percolator for testing by @ypriverol in #293
• updating nextflow.config by @ypriverol in #294
• Feature/bruker data by @jspaezp in #275
• First iteration of bug fixing in Bruker support by @ypriverol in #295
• pmultiqc 0.21 -> 0.22 by @ypriverol in #297
• major refactoring of PLFQ to a probabilistic approach by @ypriverol in #300
• error fixed docker hub diann by @ypriverol in #302
• Dev by @ypriverol in #304
• Dev by @ypriverol in #305
• Add warning info and set mass accurancy automatic for DIA when Dalton input(Don't merge) by @daichengxin in #306
• fixed errors by @daichengxin in #307
• Release of Openms 3.1.0 by @ypriverol in #308
• Dev by @ypriverol in #310
• Fallback version reporting of zip by @jspaezp in #312
• Feature/retain final speclib by @jspaezp in #313
• update dda and bruker report by @daichengxin in #314
• Error fix in msgf+ module. by @ypriverol in #316
• Improving doc by @daichengxin in #319
• standardize spectrum identifier for bruker data by @daichengxin in #321
• fixed multiple bugs and nf-template by @daichengxin in #331
• feature/skip preliminary analysis on dia by @jspaezp in #335
• library creation by @daichengxin in #341
• changes in figure, update. by @ypriverol in #348
• Dev by @ypriverol in #352
• Reduce staging overhead on subset workflows by @jspaezp in #355
• update template 2.13 by @ypriverol in #353
• sdrf-pipelines 0.0.24 -> 0.0.25 by @ypriverol in #356
• Chymotrypsin -> Chymotrypsin/P in MSGF+ by @ypriverol in #357
• Template update 2.13.1 by @ypriverol in #358
• pmultiqc 0.0.25 by @ypriverol in #359
• pmultiqc 0.0.24 by @ypriverol in #360
• first PR about identification subworkflow by @daichengxin in #351
• This PR add the parameter of charge to SAGE processor and other properties by @ypriverol in #363
• sdrf-pipelines 0.0.25 -> 0.0.26 by @ypriverol in #365
• MonoIsotopic mass for DIANN peptides with unknown AA by @ypriverol in #369
• add optional ms2rescore step by @daichengxin in #362
• Add dda id ci and fixed some bugs by @daichengxin in #373
• add msgfdb_indexing by @daichengxin in #374
• ms2rescore for quant workflow and fixed some bugs by @daichengxin in #378
• [HOTFIX] pipeline failing without id_only because of missing outputs by @jpfeuffer in #382
• Bug/samplecheck by @daichengxin in #387
• Make validation of ontology terms optional by @wfondrie in #386
• Update sdrf-pipelines 0.0.26 -> 0.0.27 by @ypriverol in #388
• diann 1.8.1 -> 1.9.1dev by @daichengxin in #389
• Add verification for tar unpacking by @wfondrie in #396
• first commit msstatistics csv -> parquet [DO NOT MERGE] by @ypriverol in #391
• sdrf-pipelines to 0.0.29 by @ypriverol in #397
• Make files selected with random_preanalysis reproducible. by @wfondrie in #400
• Migration from python in house scripts to quantms-utils by @ypriverol in #398
• Update branch from dev by @ypriverol in #401
• Minor changes including docs and nextflow configs by @ypriverol in #403
• add spectrum2feature by @daichengxin in #404
• tdf2mzml in bigbio by @ypriverol in #407
• quantms-utils 0.0.8 -> 0.0.9 by @ypriverol in #409
• clean and optimization by @daichengxin in #412
• minor updating doc by @daichengxin in #413
• Remove tests that depend on nf-core TOKENS by @ypriverol in #414
• Release of quantms v1.3.0 by @ypriverol in #405

New Contributors

• @WangHong007 made their first contribution in #205
• @fabianegli made their first contribution in #222
• @jspaezp made their first contribution in #275
• @wfondrie made their first contribution in #386

Full Changelog: https://github.com/bigbio/quantms/commits/v1.3.0