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nf-core/quantms: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[1.3.0] nfcore/quantms - [08/04/2024] - Santiago de Cuba

Added

  • #335 (Performance improvement) Improvements in DIA pipeline to use random/subset files for library search
  • #351 Identification workflow for DDA data

Changed

  • #365 Updated sdrf-pipelines==0.0.26
  • #359 Updated pmultiqc==0.0.25

Fixed

  • #357 Chymotrypsin -> Chymotrypsin/P in MSGF+
  • #355 Fixes bin/diann_convert.py
  • #316 Fixing MSGF+ error

Dependencies

Parameters

  • 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
  • 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

Deprecations

[1.2.0] nfcore/quantms - [11/02/2023] - Thimphu

Added

Changed

  • #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

Fixed

Dependencies

  • New dependency on sage search engine.

Parameters

  • 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)

[1.1.1] nfcore/quantms - [03/27/23] - Berlin-Bern

Added

  • #92 Improved output docs for mzTab
  • #91 Added dev profile for nightly versions of OpenMS tools

Changed

  • #88 Updated Comet version to latest release (2023010)

Fixed

  • #93 Fixed bug in docker vs. singularity container logic in some processes.

[1.1.0] nfcore/quantms - [03/20/2023] - Berlin

  • 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

Added

  • #176 - Add name of each ID step
  • #205 - mzTab export for DIANN outputs

Changed

  • #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

Fixed

  • #187 - Bug fixing in proteomicsLFQ applying FDR at PSM level
  • #207 - Bug fixing in dissociation method translation for Luciphor

Dependencies

  • #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.

Parameters

  • #193 - Set the local_input_type default parameter to mzML
  • #212 - Set the min_consensus_support default parameter to 1 to filter in ConsensusID for peptides identified with both search engines
  • #200 - Add export_mztab parameter to allow to run PROTEINQUANTIFIER TMT without exporting to mzTab

[1.0] nfcore/quantms - [05/02/2022] - Havana

Initial release of nf-core/quantms, created with the nf-core template.

Added

  • 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

Fixed

  • This is the first release - no reported issues

Dependencies

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