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#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)
#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)
#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)
#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)
#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
Tool
Previous version
New version
KMCP
0.9.1
0.9.4
TAXPASTA
0.6.1
0.7.0
Deprecated
#492 Removed --kmcp_mode parameter from KMCP to allow per database specification by setting in db_params in database sheet (fixed by @jfy133)
#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)
#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)