Version history

Added Feature

  • #275 BigBio Added support for bruker data in DIA branch @daichengxin @ypriverol @jspaezp.
  • #275 BigBio And speed-up to DIA-NN pipeline @jspaezp.
  • #275 BigBio Support for library-base search in DIA-NN pipeline @jspaezp.
  • #300 BigBio Major refactoring of LFQ-DDA MBR algorithm @jpfeuffer @ypriverol @timosachsenberg.
  • #279 BigBio Support for SAGE search engine @jpfeuffer @timosachsenberg @ypriverol.
  • #122 BigBio Update openms 3.1.0 by @ypriverol @timosachsenberg

Changed

  • #314 Update for pmultiqc to pmultiqc=0.0.23 @WangHong007 @daichengxin
  • #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

### Additional changes

Full Changelog: https://github.com/nf-core/quantms/compare/1.1.1…1.2.0

What’s Changed

New Contributors

Full Changelog: 1.1.0…1.1.1

These release includes the following major changes:

  • 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

What’s Changed

New Contributors

Full Changelog: 1.0…1.1.0

[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.

DependencyVersion
thermorawfileparser1.3.4
comet2021010
msgf+2022.01.07
openms2.8.0
sdrf-pipelines0.0.21
percolator3.5
pmultiqc0.0.11
luciphor2020_04_03
dia-nn1.8.1
msstats4.2.0
msstatstmt2.2.0

Deprecated

New Contributors

Full Changelog: https://github.com/nf-core/quantms/commits/1.0