v1.1.4

Added

• pluspf8, ncbi_16s_18s_28s_ITS databases
• Add all sample tool combinations to report

Changed

• Enable kraken2 by default
• Clarify error messages

Fixed

• Handle no assignments bracken error

v1.1.3

Added

• New docs format.
• Render bokeh.

v1.1.2

Changed

• Update nextflow_schema.json

v1.1.1

Fixed

• Overriding taxonomy now works correctly
• Added missing threads param to kraken2

v1.1.0

Added

• Report now includes dynamic sankey visualisation and table
• Nextflow schema

Changed

• Updated to use new fastqingress module, permitting single .fastq input
• Rewired DAG to rely on sample id's rather than filenames

Fixed

• Handle bracken failure when there are no classifications
• Handle cyclic dag issue when taxonomy has duplicate names

v1.0.0

First release.

v0.2.1

Changed

• Updated project to use latest practices from wf-template.

Fixed

• Bug fix for empty taxids in split by clade rules.
• Incorrect specification of conda environment file in Nextflow config.

v0.2.0

Added

• Help message when required parameters are not given.
• --split to customise partitioning of output fastq data

Changed

• Now uses ncbitaxonomy rather than ete3
• Outputs dirs within fastq_bundles containing reads partitioned by
  rules specified by --split

v0.1.0

Added

• Help message when required parameters are not given
• --download command to download other sample metagenomic databases
• --threads to change number of threads given to centrifuge

Changed

• README example command now refers to the zymo db rather hvpc
• --reads param changed to --fastq
• Performance improvement to split_by_master.py

v0.0.2

Added

• New minimal centrifuge database included with the project
• New minimal sample dataset for testing

Changed

• Report reads stats section using standard aplanat report section

Removed

• Report section comparing unclassified vs classified reads removed