The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- 627 Move thermorawfileparser and onsite modules from local to bigbio/nf-modules
- 629 Update quantms-rescoring to 0.0.13 to support transfer learning
- 615 Update quantms-utils 0.0.24 and pmultiqc 0.0.39
- 614 Changed enable_diann_mztab default from true to false. For DIA pipelines the mzTab will not be generated unless specified by a parameter
--enable_diann_mztab true. - 635 Minimum Nextflow version requirement updated to
>=25.04.0
- Updated quantms-rescoring==0.0.13
- Updated pmultiqc==0.0.39
- Updated pyonsite==0.0.2
- Updated quantms-utils==0.0.24
- 626 Removed luciphor-specific parameters:
luciphor_neutral_losses,luciphor_decoy_mass,luciphor_decoy_neutral_losses. These have been replaced with onsite parameters:onsite_neutral_losses,onsite_decoy_mass,onsite_decoy_neutral_losses. The new onsite module provides support for multiple PTM localization algorithms (AScore, PhosphoRS, and LucXor) with unified parameter naming. See the Migration Guide in the documentation for a complete parameter mapping table and migration instructions.
- 571 Added AlphaPeptDeep to quantms rescoring
- 564 Small patch with DIA precursor and fragment masses limits
- 567 Update nf-core template to 3.3.2
- 560 Improvements in the documentation
- Renamed
ms2pip_model_dir→ms2_model_dir - Renamed
ms2pip_model→ms2_model
- 568, 570 Multiple bugs fixed for pmultiqc library, multiple PRs, final version updated to version 0.0.33
- Updated quantms-rescoring==0.0.12
- Updated pmultiqc==0.0.33
- #555 Added support for methionine excision to COMET and DIANN.
- 551 Standardization of names in meta.yml for all tools & Big refactoring for all modules to subfolders
- #547 Minor refinements with quantms code style, update msstats LFQ -> 4.14.0
- #539 quantms-utils 0.0.23 & sdrf-pipelines 0.0.32. This includes a fix for TMT-labelled samples.
- #541 add mztab to results for pmultiqc
- #547 Refinements of quantms code style
- #545 small bug in SNR step
- #544 Fixing bug issues with SNR; quantms-utils -> quantms-rescoring
- #543 add Fabian Egli as contributor
- #542 pmultiqc version increased to 0.0.28. Error fixed with diann_report.tsv
- #537 pmultiqc updated 0.0.27 version
- #536 update pmultiqc to 0.0.27
- #531 Update for README.md Review effort 1/5
- Updated quantms-utils to version 0.0.23
- Updated bioconductor-msstats to version 4.14.0
- Updated pmultiqc to version 0.0.28
- Updated sdrf-pipelines to version 0.0.32
- #423 Support for plex Correction matrices for TMT and iTRAQ analytical methods.
- #485 Support for DIANN 2.0.2
- #494 Generation of mzml feature files for Deeplearning and AI tools, algorithm and description in quantms-utils
- #489 Smart rescoring of peptide identifications using deepLC and ms2pip, enabling RT training and model fitting. read the details in quantms-rescoring
- #474 Updated OpenMS==3.3.0
- #485 Support for DIA-NN 2.0
- #489 Refactor quantms-rescoring
- #456 Optimization of process resources
- #454 Output all DIA-NN results files
- #482 Fixed TMT MS3
- #483 Fixed ms2rescore log file name
- #420 Fixed MSGFDB index memory error
- #485 Fixed DIA-NN results format conversion
- openms==3.3.0
- thermorawfileparser==1.4.5
- quantms-utils==0.0.21
- diann==2.0.2
- quantms-rescoring==0.0.7
- ms2rescore==3.1.4
- ms2pip>=4.0
- deepLC>=3.0
- isotope_correction: Enable isotope correction
- plex_corr_matrix_file: Path to the correction matrix file for isobaric labelling, defaults are in assets folder
- quant_activation_method: Operate only on MSn scans where any of its precursors features a certain activation method
- ms2_fragment_method: The fragmentation method used during tandem MS
- diann_report_decoys: Save decoy PSMs to the main .parquet report for DIA-NN 2.0
- diann_export_xic: Instructs DIA-NN to extract MS1/fragment chromatograms for identified precursors
- mzml_features: Allows generating for MS1 features maps for every mzml file analyzed.
- #450 Removes the posterior_probabilities parameter
- #335 (Performance improvement) Improvements in a DIA pipeline to use random/subset files for library search
- #351 Identification workflow for DDA data
- #362 Introduction to ms2rescore to identification workflow
- #374 Add msgf+ database indexing step
- #378 Introduction to ms2rescore to quant workflow
- #386 Make validation of ontology terms optional
- #398 Python scripts moved to quantms-utils package
- #389 Introduction to DIANN 1.9.1 to the pipeline, only available in Singularity.
- #396 Adds a verification step to unpacking tar archives in the DECOMPRESS process
- #397 More options included in SDRF validation.
- #404 Add spectrum SNR features to rescore
- #365 Updated sdrf-pipelines==0.0.29
- #359 Updated pmultiqc==0.0.25
- #391 Move mzML statistics to parquet files from csv
- #386 Make optional the validation of ontology terms in the input SDRF file
- #374 Create the common msgf+ database in one step before the msgf+ runs on each ms run file.
- #357 Chymotrypsin -> Chymotrypsin/P in MSGF+.
- #355 Fixes bin/diann_convert.py
- #316 Fixing MSGF+ error.
- #396 Added verification of tar archive unpacking to prevent silent failures.
- #400 The random file selection when using
random_preanalysiswith DIANN is now reproducible.
- quantms-utils==0.0.10
- diann==1.9.1
- id_only: Only perform identification, no quantification
- min_peaks: Minimum number of peaks in a spectrum to be considered for search
- export_decoy_psm: Export decoy PSMs
- skip_rescoring: Skip rescoring steps
- skip_preliminary_analysis: Skip preliminary analysis in DIA-NN
- empirical_assembly_log: Path to the empirical assembly log file
- random_preanalysis: Use random/subset files for library search
- empirical_assembly_ms_n: Number of MS runs to use for empirical assembly
- validate_ontologies: Enable or disable validating ontologies in the input SDRF file
- skip_ms_validation: Skip validation of mass spectrometry files
- skip_factor_validation: Skip validation of factor columns
- skip_experimental_design_validation: Skip validation of experimental design
- use_ols_cache_only: Use cached version of the Ontology Lookup Service
- ms2rescore: Whether performing peptide identification rescoring with LC-MS predictors such as MS²PIP and DeepLC
- ms2pip_model_dir: The path of ms2pip model files
- rescore_range: Rescoring for independent run, Sample or whole experiments
- ms2pip_model: Which deep learning model to generate feature
- feature_generators: Which feature generator to generate feature
- calibration_set_size: Percentage of number of calibration set for DeepLC
- add_snr_feature_percolator: Whether add signal-to-noise ratio features for identification rescoring in percolator
- diann_version: The version of DIA-NN used
- random_preanalysis_seed: Set the random seed for the random selection of spectrum files to generate the empirical library
- #275 BigBio Added support for bruker data in DIA branch.
- #275 BigBio And speed-up to DIA-NN pipeline.
- #275 BigBio Support for library-base search in DIA-NN pipeline.
- #300 BigBio Major refactoring of LFQ-DDA MBR algorithm.
- #279 BigBio Support for SAGE search engine.
- #314 Update for pmultiqc to pmultiqc=0.0.23
- #308 Update for openms to openms=3.1.0
- Update for sdrf-pipelines to sdrf-pipelines=0.0.24
- Update for msstats to msstats=4.2.1
- #316 Fixed jar path selection of luciphoradapter and msgf+
- Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
- Fixed multiple bugs Pull Request #293 BigBio, #279 BigBio, #265 BigBio, #260 BigBio, #257 BigBio
- New dependency on
sagesearch engine.
- feature_with_id_min_score: Minimum score of a feature with a peptide identification (default: 0.10)
- feature_without_id_min_score: Minimum score of a feature without peptide identification (transfer feature, default: 0.75)
- lfq_intensity_threshold: Minimum intensity of a feature to be considered in the MBR algorithm (default: 1000)
- sage_processes: Number of processes to use in SAGE search engine (default: 1)
- diann_speclib: Path to the spectral library to use in DIA-NN (default: null)
- convert_dotd: if convert .d file to mzml (default: false)
- #88 Updated Comet version to latest release (2023010)
- #93 Fixed bug in docker vs. singularity container logic in some processes.
- Bugfixes and speed increases in the OpenMS tools due to version update to 2.9.1
- Improvements in logging by adding many more process.ids
- Large restructuring of DIA branch to increase parallelizability
- Better error handling in MSstats step plus new parameter to filter for MSstats' adjusted p-value in the plots
- More efficient parsing of mzML statistics in a separate step
- A clearer distinction between per-run and experiment-wide FDRs with one parameter for each
- More test profiles including larger "full" tests
- #169 - Restruct DIA-NN step1 : Generate an in silico predicted spectral library
- #178 - Restruct DIA-NN step2 : Preliminary analysis of individual raw files
- #179 - Restruct DIA-NN steps 3-5 to be as parallel as possible
- #200 - Rename MSstats/Triqler/mzTab input and output
- #187 - Bug fixing in proteomicsLFQ applying FDR at PSM level
- #207 - Bug fixing in dissociation method translation for Luciphor
- #203 - update openms dependency -> 3.0.0dev
- #208 - update pmultiqc dependency -> 0.0.13. Support for DIANN in pmultiqc and enable the generation of search engine scores distributions/peptide and protein table by pmultiqc.
- #193 - Set the
local_input_typedefault parameter tomzML - #212 - Set the
min_consensus_supportdefault parameter to1to filter in ConsensusID for peptides identified with both search engines - #200 - Add
export_mztabparameter to allow torun PROTEINQUANTIFIER TMT without exporting to mzTab
Initial release of bigbio/quantms, created with the nf-core template.
- New pipeline for DDA-LFQ data analysis
- New pipeline for DDA-ISO data analysis
- New datasets for DDA-LFQ and DDA-ISO data analysis
- Documentation added for DDA pipeline
- First pipeline for DIA-LFQ data analysis
- This is the first release - no reported issues
The pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
| Dependency | Version |
|---|---|
thermorawfileparser |
1.3.4 |
comet |
2021010 |
msgf+ |
2022.01.07 |
openms |
3.1.0 |
sdrf-pipelines |
0.0.26 |
percolator |
3.5 |
pmultiqc |
0.0.24 |
luciphor |
2020_04_03 |
dia-nn |
1.8.1 |
msstats |
4.10.0 |
msstatstmt |
2.10.0 |