What's Changed

• Add new modules by @daichengxin in Add new modules #1
• Add input subworkflow and thermorawfileparser by @daichengxin in Add input subworkflow and thermorawfileparser #3
• Add DatabaseSearchEngines Subworkflow by @daichengxin in Add DatabaseSearchEngines Subworkflow #14
• Add PSMRescoring、PSMFDRControl、Phosphoscoring、ProteinInference、Featur... by @daichengxin in Add PSMRescoring、PSMFDRControl、Phosphoscoring、ProteinInference、Featur... #18
• docker openms 6.0 -> 2.7pre by @ypriverol in docker openms 6.0 -> 2.7pre #19
• Add LFQ part and fixed bugs by @daichengxin in Add LFQ part and fixed bugs #20
• add pmulitqc by @daichengxin in add pmulitqc #21
• fixed bug and publish files by @daichengxin in fixed bug and publish files #22
• Improve docs by @ypriverol in Improve docs #23
• minor changes by @ypriverol in minor changes #25
• docs by @ypriverol in docs #26
• docs by @ypriverol in docs #27
• docs improvements by @ypriverol in docs improvements #28
• docs by @ypriverol in docs #29
• docs by @ypriverol in docs #30
• docs by @ypriverol in docs #31
• dcos by @ypriverol in dcos #32
• docs by @ypriverol in docs #33
• clean docs by @ypriverol in clean docs #34
• quantms by @ypriverol in quantms #40
• minor changes by @ypriverol in minor changes #41
• improvements by @ypriverol in improvements #42
• improvements conda by @ypriverol in improvements conda #43
• improvements conda by @ypriverol in improvements conda #44
• improvements by @ypriverol in improvements #45
• improvements by @ypriverol in improvements #46
• conda improvements by @ypriverol in conda improvements #47
• improve conda by @ypriverol in improve conda #49
• conda by @ypriverol in conda #50
• update name by @daichengxin in update name #51
• output msgf and comet idxml file by @daichengxin in output msgf and comet idxml file #52
• conda increase to 0.0.19 by @ypriverol in conda increase to 0.0.19 #53
• openms-2.7 in bioconda by @ypriverol in openms-2.7 in bioconda #54
• openms in bioconda by @ypriverol in openms in bioconda #55
• openms-2.7 in bioconda by @ypriverol in openms-2.7 in bioconda #56
• rollback inference by @ypriverol in rollback inference #57
• update quantms by @daichengxin in update quantms #59
• idmapper changes by @ypriverol in idmapper changes #60
• ebicluster by @ypriverol in ebicluster #61
• fixed by @ypriverol in fixed #63
• minor change by @ypriverol in minor change #64
• TMT improvements using openms=2.8.0dev by @ypriverol in TMT improvements using openms=2.8.0dev #67
• Add output files by @daichengxin in Add output files #70
• forgot image by @jpfeuffer in forgot image #72
• manual merge of the template update 2.2 branch by @jpfeuffer in manual merge of the template update 2.2 branch #73
• version fix by @daichengxin in version fix #78
• remove multiqc by @daichengxin in remove multiqc #82
• add DIA workflow by @daichengxin in add DIA workflow #112
• update meta.nf by @daichengxin in update meta.nf #116
• fixed error by @daichengxin in fixed error #124
• diann container from ypriverol -> biocontainers by @ypriverol in diann container from ypriverol -> biocontainers #118
• Template 2.3 update by @ypriverol in Template 2.3 update #126
• Utils updated by @ypriverol in Utils updated #128
• Documentation for nf-core by @ypriverol in Documentation for nf-core #129
• DIA improvement by @daichengxin in DIA improvement #132
• minor changes to improve CI speed by @ypriverol in minor changes to improve CI speed #133
• increase min_peptide in test by @ypriverol in increase min_peptide in test #134
• minor fix by @daichengxin in minor fix #135
• Template updated 2.3.1 by @ypriverol in Template updated 2.3.1 #139
• Template update 2.3.2 by @jpfeuffer in Template update 2.3.2 #142
• updates by @ypriverol in updates #143
• Major fix by @daichengxin in Major fix #145
• pull nf-core and update pmultiqc by @daichengxin in pull nf-core and update pmultiqc #152
• add DIA triqler and MSstats by @daichengxin in add DIA triqler and MSstats #153
• diann 1.8.1 by @ypriverol in diann 1.8.1 #154
• skip msstats tests in PTM tests by @ypriverol in skip msstats tests in PTM tests #155
• Master by @ypriverol in Master #157
• Enhancement/logging by @daichengxin in Enhancement/logging #161
• [FIX] AWS and conda by @jpfeuffer in [FIX] AWS and conda #163
• add MSstatsTMT and update MSstats by @daichengxin in add MSstatsTMT and update MSstats #158
• Tests changed, move them to test-datasets by @ypriverol in Tests changed, move them to test-datasets #167
• Sync with nf-core by @jpfeuffer in Sync with nf-core #170
• Sync with nf-core by @jpfeuffer in Sync with nf-core #174
• refactor DIA-NN step 1 by @daichengxin in refactor DIA-NN step 1 #169
• add name of each ID step by @daichengxin in add name of each ID step #176
• restruct DIA-NN step2 by @daichengxin in restruct DIA-NN step2 #178
• Restruct DIA-NN step 3,4,5 by @daichengxin in Restruct DIA-NN step 3,4,5 #179
• Diann update by @ypriverol in Diann update #182
• Changelog and DIA-NN double-check by @daichengxin in Changelog and DIA-NN double-check #184
• [Docu] update metro by @jpfeuffer in [Docu] update metro #185
• [FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. by @jpfeuffer in [FIX/FEATURE] Add exp. wide PSM-FDR. Rename FDR params. Slightly change usage. #187
• enforce style and add aws test by @daichengxin in enforce style and add aws test #186
• minor fixed by @daichengxin in minor fixed #193
• quick fix by @daichengxin in quick fix #195
• rename output by @daichengxin in rename output #200
• add msstats_in by @daichengxin in add msstats_in #204
• Update main.nf by @ypriverol in Update main.nf #203
• fixed by @daichengxin in fixed #207
• update pmultiqc by @daichengxin in update pmultiqc #208
• Added the decoys to TMT output by @ypriverol in Added the decoys to TMT output #210
• enable mzTab for DIA-NN by @WangHong007 in enable mzTab for DIA-NN #205
• print warning info when run DIA-NN with conda by @daichengxin in print warning info when run DIA-NN with conda #212
• fix version by @daichengxin in fix version #213
• small fixs by @WangHong007 in small fixs #218
• Upgrade 2.5.1 template by @ypriverol in Upgrade 2.5.1 template #220
• Tetsrun by @fabianegli in Tetsrun #222
• Code maintenance by @fabianegli in Code maintenance #221
• Update pmultiqc module to 0.0.14 by @ypriverol in Update pmultiqc module to 0.0.14 #225
• Test pmultiqc v0.0.15 to see if it works by @WangHong007 in Test pmultiqc v0.0.15 to see if it works #226
• testing with dev version of OpenMS 2.8.0 by @ypriverol in testing with dev version of OpenMS 2.8.0 #229
• dynamic version by @WangHong007 in dynamic version #230
• Fix config warnings by @jpfeuffer in Fix config warnings #232
• fixed bugs by @daichengxin in fixed bugs #234
• improve sdrf validation hint by @daichengxin in improve sdrf validation hint #237
• enable spectra_ref in mzTab by @WangHong007 in enable spectra_ref in mzTab #240
• pmultiqc move from 0.0.17 -> 0.0.18 by @ypriverol in pmultiqc move from 0.0.17 -> 0.0.18 #242
• pmultiqc:0.0.18 -> 0.0.19 by @ypriverol in pmultiqc:0.0.18 -> 0.0.19 #249
• Add max_missed_cleavages option to msgf by @jpfeuffer in Add max_missed_cleavages option to msgf #245
• add msstats threshold by @daichengxin in add msstats threshold #252
• Parallel mzml_statistics by @WangHong007 in Parallel mzml_statistics #257
• Reduce memory usage in diann_convert by @WangHong007 in Reduce memory usage in diann_convert #260
• Major update of latest template from nf-core by @ypriverol in Major update of latest template from nf-core #262
• Dev by @ypriverol in Dev #264
• small change. by @ypriverol in small change. #265
• Fixing multiple bugs of sage quantms by @ypriverol in Fixing multiple bugs of sage quantms #279
• Dev by @ypriverol in Dev #281
• sdrf-pipelines version 0.0.24 and parameters for msstats tmt by @ypriverol in sdrf-pipelines version 0.0.24 and parameters for msstats tmt #284
• update some process to openms dev by @ypriverol in update some process to openms dev #289
• Dev by @ypriverol in Dev #291
• id transfer threshold update by @ypriverol in id transfer threshold update #292
• updating percolator for testing by @ypriverol in updating percolator for testing #293
• updating nextflow.config by @ypriverol in updating nextflow.config #294
• Feature/bruker data by @jspaezp in Feature/bruker data #275
• First iteration of bug fixing in Bruker support by @ypriverol in First iteration of bug fixing in Bruker support #295
• pmultiqc 0.21 -> 0.22 by @ypriverol in pmultiqc 0.21 -> 0.22 #297
• major refactoring of PLFQ to a probabilistic approach by @ypriverol in major refactoring of PLFQ to a probabilistic approach #300
• error fixed docker hub diann by @ypriverol in error fixed docker hub diann #302
• Dev by @ypriverol in Dev #304
• Dev by @ypriverol in Dev #305
• Add warning info and set mass accurancy automatic for DIA when Dalton input(Don't merge) by @daichengxin in Add warning info and set mass accurancy automatic for DIA when Dalton input(Don't merge) #306
• fixed errors by @daichengxin in fixed errors #307
• Release of Openms 3.1.0 by @ypriverol in Release of Openms 3.1.0 #308
• Dev by @ypriverol in Dev #310
• Fallback version reporting of zip by @jspaezp in Fallback version reporting of zip #312
• Feature/retain final speclib by @jspaezp in Feature/retain final speclib #313
• update dda and bruker report by @daichengxin in update dda and bruker report #314
• Error fix in msgf+ module. by @ypriverol in Error fix in msgf+ module. #316
• Improving doc by @daichengxin in Improving doc #319
• standardize spectrum identifier for bruker data by @daichengxin in standardize spectrum identifier for bruker data #321
• fixed multiple bugs and nf-template by @daichengxin in fixed multiple bugs and nf-template #331
• feature/skip preliminary analysis on dia by @jspaezp in feature/skip preliminary analysis on dia #335
• library creation by @daichengxin in library creation #341
• changes in figure, update. by @ypriverol in changes in figure, update. #348
• Dev by @ypriverol in Dev #352
• Reduce staging overhead on subset workflows by @jspaezp in Reduce staging overhead on subset workflows #355
• update template 2.13 by @ypriverol in update template 2.13 #353
• sdrf-pipelines 0.0.24 -> 0.0.25 by @ypriverol in sdrf-pipelines 0.0.24 -> 0.0.25 #356
• Chymotrypsin -> Chymotrypsin/P in MSGF+ by @ypriverol in Chymotrypsin -> Chymotrypsin/P in MSGF+ #357
• Template update 2.13.1 by @ypriverol in Template update 2.13.1 #358
• pmultiqc 0.0.25 by @ypriverol in pmultiqc 0.0.25 #359
• pmultiqc 0.0.24 by @ypriverol in pmultiqc 0.0.24 #360
• first PR about identification subworkflow by @daichengxin in first PR about identification subworkflow #351
• This PR add the parameter of charge to SAGE processor and other properties by @ypriverol in This PR add the parameter of charge to SAGE processor and other properties #363
• sdrf-pipelines 0.0.25 -> 0.0.26 by @ypriverol in sdrf-pipelines 0.0.25 -> 0.0.26 #365
• MonoIsotopic mass for DIANN peptides with unknown AA by @ypriverol in MonoIsotopic mass for DIANN peptides with unknown AA #369
• add optional ms2rescore step by @daichengxin in add optional ms2rescore step #362
• Add dda id ci and fixed some bugs by @daichengxin in Add dda id ci and fixed some bugs #373
• add msgfdb_indexing by @daichengxin in add msgfdb_indexing #374
• ms2rescore for quant workflow and fixed some bugs by @daichengxin in ms2rescore for quant workflow and fixed some bugs #378
• [HOTFIX] pipeline failing without id_only because of missing outputs by @jpfeuffer in [HOTFIX] pipeline failing without id_only because of missing outputs #382
• Bug/samplecheck by @daichengxin in Bug/samplecheck #387
• Make validation of ontology terms optional by @wfondrie in Make validation of ontology terms optional #386
• Update sdrf-pipelines 0.0.26 -> 0.0.27 by @ypriverol in Update sdrf-pipelines 0.0.26 -> 0.0.27 #388
• diann 1.8.1 -> 1.9.1dev by @daichengxin in diann 1.8.1 -> 1.9.1dev #389
• Add verification for tar unpacking by @wfondrie in Add verification for tar unpacking #396
• first commit msstatistics csv -> parquet [DO NOT MERGE] by @ypriverol in first commit msstatistics csv -> parquet [DO NOT MERGE] #391
• sdrf-pipelines to 0.0.29 by @ypriverol in sdrf-pipelines to 0.0.29 #397
• Make files selected with random_preanalysis reproducible. by @wfondrie in Make files selected with random_preanalysis reproducible. #400
• Migration from python in house scripts to quantms-utils by @ypriverol in Migration from python in house scripts to quantms-utils #398
• Update branch from dev by @ypriverol in Update branch from dev #401
• Minor changes including docs and nextflow configs by @ypriverol in Minor changes including docs and nextflow configs #403
• add spectrum2feature by @daichengxin in add spectrum2feature #404
• tdf2mzml in bigbio by @ypriverol in tdf2mzml in bigbio #407
• quantms-utils 0.0.8 -> 0.0.9 by @ypriverol in quantms-utils 0.0.8 -> 0.0.9 #409
• clean and optimization by @daichengxin in clean and optimization #412
• minor updating doc by @daichengxin in minor updating doc #413
• Remove tests that depend on nf-core TOKENS by @ypriverol in Remove tests that depend on nf-core TOKENS #414
• Release of quantms v1.3.0 by @ypriverol in Release of quantms v1.3.0 #405

New Contributors

• @WangHong007 made their first contribution in enable mzTab for DIA-NN #205
• @fabianegli made their first contribution in Tetsrun #222
• @jspaezp made their first contribution in Feature/bruker data #275
• @wfondrie made their first contribution in Make validation of ontology terms optional #386

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