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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.

[3.1.0] - In development

Added

  • New profile for use on CTMR Gandalf, ctmr_gandalf.
  • Kraken2 added for taxonomic profiling, replaces sendsketch as contamination screen.
  • Docker profile

Changed

  • Renamed profile for CTMR-NAS to ctmr_nas to better conform to incoming profiles.
  • Moved contig renaming script to shovill process from contamination screen process.
  • Now publishes shovill.log in the output directory by default.
  • Limited the search scope for MultiQC to minimize risk of process timeouts on HPC systems.

Removed

  • Sendsketch replaced with Kraken2

[3.0.0] - 2021-01-15

Added

  • A script was implemented that renames the headers of fasta-files.
  • New optional flags to lessen storage use: --keep_trimmed_fastq will allow output of trimmed reads (default = not saved) --keep_shovill_output will output the assemblies from shovill, in conjunction with assembled genomes from prokka (default = only from prokka)
  • Contamination screen is now parsed and used as taxonomic info for prokka.
  • MultiQC now incorporates the trimmed QC reports as well.
  • User now receives a file with compiled assemblystats, generated via BBmap's statswrapper.

Changed

  • QC and trimming now done by FastP, not BBduk and FastQC, resulting in a much faster runtime.
  • Contamination screening now done by Sendsketch.
  • Contamination now ascertained from assemblies, not trimmed reads.
  • BACTpipe now updated to DLS2-format.
  • Updated BACTpipe now requires a newer Nextflow version.

Removed

  • BBduk no longer used.
  • FastQC no longer used.
  • Mashscreen no longer used.

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.