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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.

[0.5.2] 2024-04-24

Fixed

  • fixed a bug in the sc2rf tables that can crash the HTML summary report

[0.5.1] 2024-03-15

Added

  • new parameters for genome QC: seq_threshold and n_threshold
    • the default values did not change

[0.5.0] 2024-03-13

Changed

  • updated default nextclade version to 3.3.1
    • default dataset version 2024-02-16--04-00-32Z
  • updated default pangolin version to 4.3
    • default pangolin-data version 1.25.1

[0.4.3] 2023-06-26

Fixed

  • fixed conda channel order
  • enhanced nextclade dataset provenance

[0.4.2] 2023-06-08

Added

  • added a DOI

[0.4.1] 2023-05-23

Changed

  • update documentation

[0.4.0] 2023-05-09

Added

  • new parameters nextclade_dataset_name and nextclade_dataset_tag for better nextclade fine tuning
    • with --update the latest dataset tag is selected
  • new filter for indels for consensus generation based on their frequency --cns_indel_filter

Fixed

  • fixed conda/mamba execution in standard profile

Changed

  • updated smallest required nextflow version to 22.10.0

[0.3.4] 2023-04-13

Changed

  • updated default nextclade version to 2.13.1
  • updated default pangolin version to 4.2 with pangolin-data version 1.18.1.1

Fixed

  • corrected column name in summary report table

[0.3.3] 2023-03-10

Added

  • timestamp in report name

[0.3.2] 2023-02-08

Fixed

  • updated conda config

[0.3.1] 2022-12-20

Added

  • added license (GPL3)

Changed

[0.3.0] 2022-12-14

Added

  • test profile
  • end-to-end CI test

Fixed

  • Report (accumulated sequence depth plot) can handle > 90 input samples

Changed

  • default reference changed from none to 'sars-cov-2'

[0.2.9] 2022-11-03

Added

  • full support for single end data

[0.2.8] 2022-09-19

Added

  • '--bamclipper_additional_parameters' option to adjust BAMClipper parameters
  • documentation on how names in the input BED file have to be to automatically generate a BEDPE file
  • added pangolin-data version to th epangolin environment/container
  • added an insert size filter for the BAM file

Fixed

  • RKI report bug

[0.2.7] 2022-08-23

Fixed

  • fixed Nextclade2 Docker auto-update

Changed

  • updated Nextclade to version 2: CoVpipe2 not compatible with nextclade version < 2.4.0
  • updated Pangolin to version 4.1.2

Removed

  • parameter pangolin_scorpio, since pangolin default behaviour changed from v4.1

[0.2.6] 2022-07-27

Fixed

  • report can handle Kraken2 output with no human, unclassified or tax_id reads

[0.2.5] 2022-07-19

Changed

  • changed bcftools consensus parameter from -I to -H I
    • does not change behaviour
  • genotype adjustment for all heterzygote variants
  • updated default pangolin version to 4.0.6
  • renamed parameter pangolin_skip_scorpio to pangolin_scorpio (default behavior of skipping scorpio does not change)
  • Kraken2 read output is not compressed - changed the file naming accordingly

Removed

  • removed unsued script
  • removed unused conda yamls

[0.2.4] 2022-06-14

Added

  • added sc2rf
    • strict params to find potential recombinants
  • added skip-scorpio parameter for pangolin
    • activeted per defaul
  • added this changelog

Changed

  • separate result tabled get published
  • better primer/reference id check
    • fist fasta id has to be at least once in the primer file (some primer kits have a non-sc2 amplicon)

[0.2.3] 2022-06-01

Changed

  • kraken2 database can be set by user
  • hard filtered variants get published in the variant calling result directory

Removed

  • removed ? removal since deletion adjustment is removed
  • update processes for pangolin and nextclade

Fixed

  • fixed container execution for pangolin and nextclade
  • fixed disabling/enabling of var_sap parameter

[0.2.2] 2022-06-01

Changed

  • updated workflow figure
  • more stable automated conda update for pangolin and nextclade directly from anaconda.org
  • updated help/readme

Removed

  • removed deletion adjustment since bcftools works as expected

[0.2.1] 2022-05-09

Added

  • LCS update functionality

[0.2.0] 2022-05-05

Added

  • LCS fro mixed sample detection

Changed

  • updated versions of samtools, liftoff, kraken, freebayes, bcftools, fastp, bedtools

Fixed

  • bedtools subtract instead of intersect for low coverage mask generation

[0.1.2] 2022-04-13

Changed

  • updated help and readme
  • disabel var-sap in default
  • removed workflow version from consensus fasta header

[0.1.1] 2022-04-07

  • fixed krona fails with mamba/conda execution
  • fixes pangolin update
  • update nextclade

[0.1.1-alpha] 2022-04-07

Added

  • DESH support

[0.1.0-alpha] 2022-04-06

  • initial commit