v2.0.9

Changed

• Update kraken databases to latest and ensure relevant taxdump is used.

Added

• Plot species richness curves.
• Provide (original and rarefied, i.e. all the samples have the same number of reads) abundance tables listing taxa per sample for a given taxonomic rank.
• Add diversity indices.
• Memory requirement help text.

v2.0.8

Fixed

• Example_cmd in config.
• Minimap2 subworkflow fixed for when no alignments.
• Remove quality 10 parameter from Minimap2 subworkflow.

v2.0.7

Fixed

• Issue where processing more than ~28 input files lead to excessive memory use.
• Minor typos in docs.

v2.0.6

Changed

• Updated description in manifest

v2.0.5

Fixed

• The version in the config manifest is up to date.

v2.0.4

Fixed

• Issue where discrepancies between taxonomy and databases led to error.

Added

• nextflow run epi2me-labs/wf-metagenomics --version will now print the workflow version number and exit.

Changed:

• Parameter name for selecting known database is now --database_set (was --source).
• Add classifier parameter and only allow running of minimap2 or kraken2 workflow.
• Workflow logic in kraken workflow has been reorganised for simpler parallelism.

Removed

• -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
• --run_indefinitely parameter removed, instead implied when --read_limit set to null.

v2.0.3

Fixed

• Add a test and fix for if all files in one directory are unclassified
• Check if fastq input exists

v2.0.2

Updated

• Use store directory for database.
• Use per file kraken_report instead of cumulative.
• Handling for unclassified with Bracken.
• Kraken2-server v0.0.8.
• Add a run indefinitely parameter.

Fixed

• Batch size breaking fastcat step.
• Consider white space in bracken report.

v2.0.1

Fixed

• Handling with kraken2 for single input file

Updated

• Removed sanitize option

v2.0.0

Updated

• Bumped base container to v0.2.0
• Kraken workflow now in real time mode with watch_path
• Kraken and Minimap now in subworkflows

Fixed

• Output argument in Fastqingress homogenised.

Changed

• Fastqingress metadata map
• Can only run Kraken or Minimap subworkflow not both
• Better help text on cli
• Fastq ingress and Args update
• Set out_dir option type to ensure output is written to correct directory on Windows