Added

• #619 Added default pipeline nf-test (added by @sofstam)
• #615 Updated to nf-core pipeline template v3.3.1 (added by @sofstam)
• #614 Updated module krakenuniq/preloadedkrakenuniq to fix preload mechanism. The RAM chunk size can now be customised on a per-database basis. (added by @muniheart with help from / ❤️ to @jfy133)
• #600 Added metaphlan to multiqc report (❤️ to @harper357 for reporting and added by @sofstam)
• #605 Added documentation on how to generate Bracken reports for different taxonomic levels (❤️ to @MajoroMask for reporting and added by @jfy133)

Fixed

• #602 Fixed a typo in the run-merging table example in usage.md (❤️ to @ilight1542 for reporting and fixed by @jfy133)
• #592 improved JSON schema for better validation (by @microlei)
• #604 KrakenUniq no longer fails due to pathname splitting during batching when only single sample supplied (by @AlexHoratio)
• #612 Fix bug with bracken results being shown in MuktiQC for long read data every if bracken not supported for long reads (added by @jfy133 and @sofstam )
• #630 Fix a bug in KRAKENUNIQ reads channel where a single-element list containing a / in the path was being split incorrectly, causing unexpected multiple list elements (❤️ to @sysbiocoder for reporting and fixed by @LilyAnderssonLee)
• #631 For paired-end reads, DIAMOND will use only the forward read file (read 1) unless reads are merged (❤️ to @sysbiocoder for reporting and fixed by @LilyAnderssonLee)
• #635 Fix faulty parsing of memory request in BBDuk (❤️ to @Proton-NTA for reporting, fix by @mahesh-panchal)

Changed

• #602 Rename (undocumented) test_nothing profile to test_minimal for consistency with other pipelines (by @jfy133)
• #614 There is now no default krakenuniq_ram_chunk_size value for KrakenUniq. By default now the entire database will be loaded into memory unless you use the parameter, or specify --preload-size in a database sheet. (added by @muniheart with help from / ❤️ to @jfy133)
• #624 Updated all relevant nf-core modules to latest version (by @sofstam)

Dependencies

Added

• #576 Sort input to krakenuniq to enable retrieval of cached batch tasks (❤️ to @muniheart for reporting and fix)
• #569 Updated to nf-core pipeline template v3.1.2 (added by @sofstam)
• #571 Updated to nf-core pipeline template v3.2.0 (added by @sofstam)

Fixed

• #580 Minor documentation typo fixes (❤️ to @AlexHoratio for reporting and fix)
• #573 Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133)
• #578 Fixed incorrect keyword in nextflow_schema.json (fix by @mashehu)
• #585 Fixed code blocks (fix by @masheshu)
• #586 Fixed wrong argument name for saving analysis reads (fix by @epstein6)

Added

• #558 Updated to nf-core pipeline template v3.1.0 (added by @LilyAnderssonLee)
• #565 Updated to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)

Fixed

• #561 Updated Centrifuge to fix internal error when running with conda (❤️ to @AnotherSimon for reporting, fix by @jfy133)

Added

• #545 Updated to nf-core pipeline template v3.0.2 (added by @LilyAnderssonLee & @jfy133)

Fixed

• #550 Fixed a bug where single-end data with the same sample names that include . in it would overwrite output files (❤️ to @SannaAb for reporting, fixed by @Midnighter)
• #552 Fixed the issue where nonpareil fails due to insufficient data for calculation caused by a missing PNG (❤️ to @Joon-Klaps for reporting, fixed by @LilyAnderssonLee)

Dependencies

Deprecated

Added

• #417 Added reference-free metagenome complexity/coverage estimation with Nonpareil (added by @jfy133)
• #466 Input database sheets can specify a db_type column to distinguish between short- and long-read databases (added by @LilyAnderssonLee)
• #505 Add small files to the file tower.yml (added by @LilyAnderssonLee)
• #508 Add nanoq as a filtering tool for nanopore reads (added by @LilyAnderssonLee)
• #511 Add porechop_abi as an alternative adapter removal tool for long reads nanopore data (added by @LilyAnderssonLee)
• #512 Update all tools to the latest version and include nf-test (updated by @LilyAnderssonLee & @jfy133)
• #537 Update the module motus/merge to the latest version (Updated by @sofstam & @LilyAnderssonLee)

Fixed

• #518 Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133)
• #523 Removed hardcoded -m lca from GANON_CLASSIFY due to more options in new version of ganon (fixed by @LilyAnderssonLee & @jfy133)
• #531 Fix FASTA input validation in schema allowing FASTQ extension, expand allowed FASTA extensions (fixed by @jfy133)
• #512 Minor formatting and ordering improvements in MultiQC report (by @jfy133)
• #532 - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133)
• #536 - Redefine contents_re for filtlong to fix its missing from the MultiQC report (fixed by @LilyAnderssonLee)

Dependencies

Deprecated

Added

• #487 Updated to nf-core pipeline template v2.14.1 (added by @jfy133)

Fixed

• #484 Improved input validation to immediately fail if run accession IDs within a given sample ID are not unique (❤️ to @sofstam for reporting, fixed by @jfy133)
• #491 Added flag to publish intermediate bracken files (❤️ to @ewissel for reporting, fixed by @sofstam and @jfy133)
• #489 Fix KrakenUniq classified reads output format mismatch (❤️ to @SannaAb for reporting, fixed by @jfy133)
• #495 Stop TAXPASTA failures when profiles do not have exact compositionality (fixes by @Midnighter, @jfy133)

Dependencies

Deprecated

• #492 Removed --kmcp_mode parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)

Added

• #477 Provide more emphasis and links to tutorials on how to retrieve and supply reference databases (❤️ to @vmkalbskopf for reporting, added by @jfy133)

Fixed

• #476 Fixed bug in validating Bracken/Kraken/KMCP split database parameters (fixed by @LilyAnderssonLee)

Dependencies

Deprecated

Added

• #454 Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam)
• #461 Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
• #461 Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
• #461 Added new parameter to optionally save uncompressed databases (added by @jfy133)
• #471 Removed -stub run in the download_pipeline.yml because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)

Fixed

• #336 Replaced samplesheet check with nf-validation for both sample and database input sheets (fix by @LilyAnderssonLee)
• #460 Corrected the channel transformations to combine Kaiju and mOTUs reports with their reference databases (fix by @Midnighter)

Added

• #439 Read deduplication with fastp (added by @maxibor)
• #440 Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)
• #442 Updated to nf-core pipeline template v2.12 (added by @sofstam)

Fixed

• #444 Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133)

Dependencies

Fixed

• #431 Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
• #430 Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)

Dependencies