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)

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

Added

• #424 Updated to nf-core pipeline template v2.11.1 (added by @LilyAnderssonLee & @sofstam)

Fixed

• #419 Added improved syntax highlighting for tables in documentation (fix by @mashehu)
• #421 Updated the krakenuniq/preloadedkrakenuniq module that contained a fix for saving the output reads (❤️ to @SannaAb for reporting, fix by @Midnighter)
• #427 Fixed preprint information in the recommended methods text (fix by @jfy133)

Dependencies

Added

• #408 Added preprint citation information to README and manifest (added by @jfy133)

Fixed

• #405 Fix database to tool mismatching in KAIJU2KRONA input (❤️ to @MajoroMask for reporting, fix by @jfy133)
• #406 Fix overwriting of bracken-derived kraken2 outputs when the database name is shared between Bracken/Kraken2. (❤️ to @MajoroMask for reporting, fix by @jfy133)
• #409 Fix a NullPointerException error occurring occasionally in older version of MEGAN’s rma2info (❤️ to @MajoroMask for reporting, fix by @jfy133)

Dependencies

Added

• #379 Added support for previously missing Bracken-corrected Kraken2 report as output (added by @hkaspersen & @jfy133 )
• #380 Updated to nf-core pipeline template v2.10 (added by @LilyAnderssonLee & @sofstam)
• #393 Add validation check for a taxpasta taxonomy directory if –taxpastaadd* parameters requested (♥️ to @alimalrashed for reporting, added by @jfy133)

Fixed

• #383 Update the module of KrakenUniq to the latest to account for edge case bugs where FASTQ input was mis-detected as wrong format (❤️ to @asafpr for reporting and solution, fixed by @LilyAnderssonLee)
• #392 Update the module of Taxpasta to support adding taxa information to results (❤️ to @SannaAb for reporting, fixed by @Midnighter)

Dependencies

Deprecated

Added

• #298 New classifier ganon (added by @jfy133)
• #312 New classifier KMCP (added by @sofstam)
• #318 New classifier MetaPhlAn4 (MetaPhlAn3 support remains) (added by @LilyAnderssonLee)
• #276 Implemented batching in the KrakenUniq samples processing (added by @Midnighter)
• #272 Add saving of final ‘analysis-ready-reads’ to dedicated directory (❤️ to @alexhbnr for request, added by @jfy133)
• #303 Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
• #308 Add citations and bibliographic information to the MultiQC methods text of tools used in a given pipeline run (added by @jfy133)
• #315 Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
• #319 Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
• #323 Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
• #345 Add simple tutorial to explain how to get up and running with an nf-core/taxprofiler run (added by @jfy133)
• #355 Add support for TAXPASTA’s --add-rank-lineage to output (❤️ to @MajoroMask for request, added by @Midnighter, @sofstam, @jfy133)
• #368 Add the ability to ignore profile errors caused by empty profiles and other validation errors when merging multiple profiles using TAXPASTA (added by @Midnighter and @LilyAnderssonLee)

Fixed

• #271 Improved standardised table generation documentation for mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
• #269 Reduced output files in AWS full test output due to very large files (fix by @jfy133)
• #270 Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
• #274 Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
• #275 Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
• #285 Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
• #286 Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
• #289 Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
• #290 Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
• #305 Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot, @jfy133)
• #304 Correct mistake in kaiju2table documentation, only single rank can be supplied (♥ to @artur-matysik for reporting, fix by @jfy133)
• #307 Fix databases being sometimes associated with the wrong tool (e.g. Kaiju) (fix by @jfy133, @Midnighter and @LilyAnderssonLee)
• #313 Fix pipeline not providing error when database sheet does not have a header (♥ to @noah472 for reporting, fix by @jfy133)
• #330 Added better tagging to allow disambiguation of Kraken2 steps of Kraken2 vs Bracken (♥ to @MajoroMask for requesting, added by @jfy133)
• #334 Increase the memory of the FALCO process to 4GB (fix by @LilyAnderssonLee)
• #332 Improved meta map stability for more robust pipeline resuming (fix by @jfy133)
• #338 Fixed wrong file ‘out’ file going to centrifuge kreport module (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
• #342 Fixed docs/usage to correctly list the required database files for Bracken and tips to obtain Kraken2 databases (fix by @husensofteng)
• #350 Reorganize the CI tests into separate profiles in preparation for implementation of nf-test (fix by @LilyAnderssonLee)
• #364 Add autoMounts to apptainer profile in nextflow.config (♥ to @hkaspersento for reporting, fix by @LilyAnderssonLee)
• #372 Update modules to use quay.io nf-core mirrored containers (♥ to @maxulysse for pointing out, fix by @LilyAnderssonLee and @jfy133)

Dependencies

Deprecated

• #338 Updated Centrifuge module to not generate (undocumented) SAM alignments by default if –save_centrifuge_reads supplied, due to a Centrifuge bug modifying profile header. SAM alignments can still be generated if --out-fmt supplied in database.csv (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)

Fixed

• #292 - Fix Taxpasta not receiving taxonomy directory (❤️ to @SannaAb for reporting, fix by @jfy133)

v1.0.0 - Dodgy Dachshund [2023-03-13]

Added

• Add read quality control (sequencing QC, adapter removal and merging)
• Add read complexity filtering
• Add host-reads removal step
• Add run merging
• Add taxonomic classification
• Add taxon table standardisation
• Add post-classification visualisation

Contributed by: @jfy133 @sofstam @Midnighter @ljmesi @MillironX @jianhong @mjamy @rafalstepien @maxibor @talnor