v2.9.3

Fixed

• Files that are empty following the fastcat filtering are discarded from downstream analyses.

v2.9.2

Fixed

• "Can only use .dt accessor with datetimelike values" error in makeReport
• "invalid literal for int() with base 10" error in makeReport

v2.9.1

Fixed

• Avoid argument list lengths that may be too long when using glob patterns.
• The Kraken2 pipeline sometimes reporting wrong numbers for unclassified counts.

v2.9.0

Fixed

• Minimum memory requirement for custom databases depends on the database size.

Added

• Workflow now accepts BAM or FASTQ files as input (using the --bam or --fastq parameters, respectively).
• Run ID's now included in the output BAM files.
• Add nextflow tags to keep track of the samples along the different processes.
• Output BAM files without host reads.

Changed

• Default for --n_taxa_barplot increased from 8 to 9.
• Replace the eCharts barplot with an equivalent Bokeh version.
• --database_set parameter is now Standard-8 when the --classifier parameter is set to kraken2.

v2.8.0

Added

• Standard 8GB kraken2 database.
• Update docs.

Fixed

• Heatmap generated when --minimap2_by_reference is enabled references with a mean coverage of less than 1% of the one with the largest value are omitted.

v2.7.0

Fixed

• Use store_dir without staging files from the web. Kraken2 can run offline if the databases have been previously stored.
• Fastcat plots showing the stats in the report before removing host sequences when --exclude_host in the minimap2 pipeline.
• Real time kraken workflow hanging indefinitely when attempting to start kraken server with too many threads.

Added

• Minimap pipeline is also able to use store_dir to store databases and run offline if the databases have been previously stored.
• Kraken2 pipeline accepts a sample sheet if the real time option is disabled.
• Only taxa present in the abundance table above the --abundance_threshold will appear in the alignment summary table (which is only generated when --minimap2_by_reference is enabled).

Removed

• --bracken_dist: the bracken additional file for the database must be included in the database folder, as it is in the kraken2 indexes and when the database is generated.
• Default local executor CPU and RAM limits

Changed

• --watch_path is now called --real_time and enables the kraken2 pipeline to classify reads as they are written with watch_path.
• The kraken2 workflow can now be used without --real_time, this will use the serverless kraken2 executable.
• Barcode directories must now be named in the format barcodeNN, where NN is at least two digits (e.g. barcode01).
• Barcode directories must now have the same number of characters (e.g. barcode01 cannot be provided with barcode001).

v2.6.1

Fixed

• Broken report when the dataframe is filtered using the --abundance_threshold.
• Taxonomy abundances barplot was not showing more abundant species.

v2.6.0

Fixed

• Broken plots caused by single quotes in NCBI taxon names.

Added

• Add the abundance_table_.tsv in the output for the last analysed rank.
• Optional --minimap2_by_reference parameter to output the sequencing depth and coverage of each matched reference in the database.

v2.5.0

Added

• --kraken_confidence to specify a threshold score.
• --exclude_host: Optional parameter can accept a FASTA/MMI file with a host reference to be excluded from the analysis.
• --include_kraken2_assignments: Output the classification of each read.

v2.4.4

Added

• --abundance_threshold : filter taxa based on their abundances.
• --n_taxa_barplot: control the number of taxa displayed in the barplot.
• Plot the taxa abundance distribution (e.g. Species abundance distribution plots).