Added

• #741 Updated to nf-core pipeline template v4.0.2 (added by @sofstam)

Fixed

• #736 Fix MultiQC silently skipping large samtools stats files by increasing log_filesize_limit in MultiQC config (reported and fixed by @Leilanasd)
• #747 Fix KrakenUniq's ext.args2 not being defined correctly (by @mahesh-panchal, @jfy133)

Dependencies

Added

• #682 Added metacache classifier and improved nf-tests (added by @sofstam)
• #559 Profiling of long reads with motus (added by @LilyAnderssonLee and @sofstam )
• #591 Add options to enable the abi option to predict adapters or provide a custom adapter list for porechop_abi (❤️ to @AlexHoratio for suggesting, fix by @LilyAnderssonLee and @sofstam)
• #595 New classifier sylph (added by @sofstam)
• #608 New classifier melon (added by @parisis and @sofstam)
• #694 Developer and contributor documentation (by @jfy133)
• #698 Add new config and nf-test for test_falcobbduk (by @jfy133)
• #699 Add new config and nf-test for test_fastpnonpareilkrakenuniq (by @jfy133)
• #703 Change stable branch name from master to main (by @jfy133)
• #705 Add new config and nf-test for test_malt (by @jfy133)
• #707 Add new config and nf-test for test_motus (by @jfy133)
• #709 Add new config and nf-test for test_nopreprocessing (by @jfy133)

Fixed

• #711 Better error strategy for the sylph classifier steps so it doesn't fail if sylph finds no hits (by @sofstam)
• #713 Improve Nextflow syntax compliance in .nf file structure (by @jfy133)
• #714 Improve nf-core linting compliance with meta.yaml files for all local subworkflows (by @jfy133)
• #730 Minor documentation fixes and updates for mOTUs, MetaPhlAn, and NONPAREIL (by @jfy133)

Changed

• #696 Switch Slack channel reporting to nf-slack plugin for AWS Megatests (by @jfy133)

Deprecated

• #710 Removed the custom script krona_cleanup due to hardcoded taxonomic ranks causing krona plots to not being properly updated. (by @sofstam)
• #698 Deprecate test_bbduk and test_falco test profiles (merged into test_falcobbduk) (by @jfy133)
• #696 Remove hook_url from the pipeline configuration, cftools#4051 (by @jfy133 and @FriederikeHanssen)
• #699 Deprecate test_fastp and test_krakenuniq test profiles (merged into test_fastpnonpareilkrakenuniq) (by @jfy133)
• #714 Renamed modules KRAKEN2_STANDARD_REPORT and KRONA_CLEANUP for consistency with nf-core guidelines (by @jfy133)

Dependencies

Added

• #678 Included metaval.config to generate input files for genomic-medicine-sweden/metaval (added by @LilyAnderssonLee)
• #655 Added nf-tests for test profile (added by @sofstam)

Fixed

• #674 Fixed bug where wrong variables names used for KrakenUniq input channel causing pipeline crash (❤️ to @pcantalupo for reporting, fixed by @jfy133)
• #675 Prevent file name conflict with mixed SE and PE runs for a single sample with stricter validation (fixed by @LilyAnderssonLee and @jfy133)
• #683 Fix pre-supplied long-read host removal index not being compatible with MINIMAP2_ALIGN module (fixed by @jfy133)

Changed

• #676 Turn off saving of BAM version of unmapped reads from long read host removal (❤️ to @sofstam for reporting, changed by @jfy133)

Dependencies

Added

• #640 Added support for saving Metaphlan SAM files (❤️ to @mr2raccoon for reporting and added by @jfy133)
• #657, #667 Template update for nf-core/tools v3.4.1 and v3.5.1 (added by @sofstam and @jfy133)

Fixed

• #653 Enable runs for PACBIO_SMRTdata (fixed by @LilyAnderssonLee)
• #657 Fix --version not printing version (❤️ to @fwa93 for reporting and added by @jfy133 )

Changed

Dependencies

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)