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CHANGELOG.md

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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.
The version numbering consists of three digits: major.minor.patch. The major version is expected to increment following major structural changes to the BACTpipe workflow. Typically, any changes to the user interface (command line arguments etc.), or output files will increment the minor version. Under-the-hood changes that do not have an impact on how end-users run our process the output will typically only increment the patch number.

Changes should fall into one of the following categories:

  • Added, for new features
  • Changed, for changes in existing functionality
  • Deprecated, for soon-to-be removed features.
  • Removed, for now removed features.
  • Fixed, for any bug fixes.

[2.8.0]

Added

Changed

Removed

Deprecated

[2.7.0] - 2019-01-16

Added

  • New command-line argument --ignore_contamination_screen will ignore all inputs that FAIL mash screen contamination check.

Changed

  • Set default errorstrategy for Nextflow to ignore.
  • Updated process declarations to use new withName syntax.

Removed

  • The intermediate output from mash screen (i.e. <sample>.mash_screen.tsv) is now removed from the output directory, in favor of the concatenated table all_samples.mash_screening_results.tsv, containing results for all samples.

Deprecated

[2.6.0] - 2018-05-28

Added

  • Created this changelog.
  • New output file, all_samples.mash_screening_results.tsv, which is a concatenation of all individual mash screening results, intended to provide a better overview of the mash screening output for all samples.

Changed

  • Created separate develop branch to contain future code development separate from the master branch, which is now considered stable.
  • Renamed mash.screen output folder to mash_screen, repacing the dot with an underscore.
  • [Docs] Added note about single (e.g. -profile) vs double dash (e.g. --reads) command line arguments.

Removed

  • Removed outdated cluster configurations for UPPMAX's now defunct Milou cluster.

Deprecated

  • The intermediate output from mash screen (i.e. <sample>.mash_screen.tsv) will be removed from the output directory in a future release.

[2.5.3b] - 2018-05-03

Changed

  • Updated assess_mash_screen.py to v0.6.1b, fixing accidental PASS of failing samples.