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CHANGELOG.md

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nf-encyclopedia Changelog

All notable changes to this project will be documented in this file.

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

[Unreleased]

[1.1.0] - 2023-04-12

Fixed

  • Fixed our conversion from EncyclopeDIA outputs to an MSstats input, which was dropping proteins due to mismatched protein accessions.

[1.0.1] - 2022-12-14

Fixed

  • Fixed issue where the docker image would not build in M1 macs.
  • Excel compatibility error due to row names in MSstats ouput.
  • Issue where the pipeline would break if non-valid R names are given.
  • Fixed and documented an issue where tests would not run locally due to a docker tag.

[1.0.0] - 2022-10-03

Changed

  • Renamed params.ms_file_csv to params.input
  • Updated EncyclopeDIA parameters to match GUI defaults.
  • Retries should automatically occur when MSconvert hangs
  • Renamed EncyclopeDIA processes to be more intuitive.
  • The group column in the input file is now optional
  • *_postfix parameters were renamed *_suffix.

Added

  • Added full support for MSstats

Fixed

  • Correctly use -a false when building a chromatogram library.
  • MSstats now outputs into the results directory.

[0.5.0] - 2022-08-26

Changed

  • Parameters updated to be more user-friendly.
  • Scripts are now in the bin directory, instead of the Docker containers.
  • Used logic from nf-core to scale resources on retries.
  • Now using the email argument again to get a custom message.
  • Removed the use of storeDir

Added

  • Reports for pipeline runs.
  • Created a public nf-encyclopedia Docker image for everything except msconvert.
  • A nearly complete system test using small mzML files.

[0.4.2] - 2022-07-19

Changed

  • Removed email argument in favor of using the default nextflow run -N <email>.
  • Removed debug and echo statements from modules.

[0.4.1] - 2022-07-12

Fixed

  • Updated GitHub Actions release workflow.

[0.4.0] - 2022-07-12

Added

  • This changelog!
  • Completely reworked pipeline since last release. Note that we were just using the main branch as our release version, but I prefer occasional manual releases for stability.