nf-core/taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

classificationilluminalong-readsmetagenomicsmicrobiomenanoporepathogenprofilingshotguntaxonomic-classificationtaxonomic-profiling

Launch version 1.2.4 https://github.com/nf-core/taxprofiler

Version history

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`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`

Tool	Previous version	New version
Nextflow	24.10.0	25.04.2
bbduk	39.06	39.18
bowtie2	2.5.2	2.5.4
bracken	2.9	3.1
diamond	2.1.8	2.1.12
fastp	0.23.0	0.24.0
ganon	2.0.0	2.1.0
kraken2	2.1.3	2.1.5
minimap2	2.28	2.29
motus	3.0.3	3.1.0
multiqc	1.27	1.30

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`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)

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`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)

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`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`

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`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`

Tool	Previous version	New version
bbmap	39.01	39.06
bowtie2	2.4.4	2.5.2
bracken	2.7	2.9
diamond	2.0.15	2.1.8
ganon	1.5.1	2.0.0
kraken2	2.1.2	2.1.3
krona	2.8	2.8.1
megan	6.24.20	6.25.9
metaphlan	4.0.6	4.1.1
minimap2	2.24	2.28
motus	3.0.3	3.1.0
multiqc	1.21	1.25
samtools	1.17	1.20

`Deprecated`

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`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`

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)

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`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`

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`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)

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`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`

Tool	Previous version	New version
Centrifuge	1.0.4_beta	1.0.4.1

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`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`

Tool	Previous version	New version
kaiju	1.8.2	1.10.0

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`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`

Tool	Previous version	New version
multiqc	1.15	1.19
fastqc	11.9	12.1
nf-validation	unpinned	1.1.3

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`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`

Tool	Previous version	New version
megan/rma2info	6.21.7	6.24.20

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`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`

Tool	Previous version	New version
KrakenUniq	1.0.2	1.0.4
taxpasta	0.6.0	0.6.1

`Deprecated`

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`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`

Tool	Previous version	New version
MultiQC	1.13	1.15
TAXPASTA	0.2.3	0.6.0
MetaPhlAn	3.0.12	4.0.6
fastp	0.23.2	0.23.4
samtools	1.16.1	1.17

`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)