nf-core/ampliseq version 2.14.0 - 2025-05-23

Summary of changes

• Multi-region analysis is now easier with custom databases, parameters were changed or added
• Updatedsbdi-gtdb,gtdb,PR2 databases and addedBOLD plant databases for classification with DADA2
• Follow nextflow's strict syntax (only impacts development)

Detailed changes

Added

• #879 - Addsbdi-gtdb=R10-RS226-1 as parameter to--dada_ref_taxonomy and make this version the default forsbdi-gtdb.
• #882 - Addgtdb=R10-RS226 as parameter to--dada_ref_taxonomy and make this version the default forgtdb.
• #883 - Add BOLD databasesplantae-bold-its1 &plantae-bold-trnL, for plant samples with markers ITS1 and trnL, versions 20240510, for DADA2 as parameter to--dada2_ref_taxonomy.
• #885 - Addpr2=5.1.0 as parameter to--dada_ref_taxonomy and make this version the default forpr2.

Changed

• #871 - Multi-region analysis is now easier with custom databases. No alignment file of the reference sequences are needed.

Fixed

• #872 - Follow nextflow's strict syntax
• #876 - Pulled the updated vsearch/clusters module from nf-core to fix a bug where a wildcard expansion trigging an arguments-too-long error.
• #878 - Downgraded nf-schema from 2.3.0 to 2.2.0 due to incompatibilities with nextflow stable versions 25.05 and newer
• #881 - Template update for nf-core/tools version 3.2.1
• #887 - Updated documentation to include all updates

nf-core/ampliseq version 2.13.0 - 2025-04-04

Summary of changes

• Zenodo changed from zenodo.org/record to zenodo.org/records and some taxonomic databases could not be downloaded any more
• Add most recent database versions for SILVA, Greengenes2, and SBDI-GTDB for DADA2 or QIIME2
• Export of a TreeSummarizedExperiment R object
• Taxonomic assignment using DADA2 is done in chunks (default 10,000 ASVs) to reduce memory and runtime
• Consensus strategy to merge or concatenate paired end reads based on overlap is introduced
• A bunch of bug fixes
• nf-core template update from 3.0.2 to 3.2.0

Detailed changes

Added

• #798 - Added SILVA version 138.2 of DADA2 taxonomy database:silva=138.2 orsilva as parameter to--dada2_ref_taxonomy
• #801 - Parameter--quality_type allows specifying the type of quality scores in raw read data, by defaultAuto (i.e. default behavior did not change)
• #804 - Added version 10 of Unite as parameter for--dada_ref_taxonomy (issue#768)
• #803,#856 - New parameters introduced related to--mergepairs_strategy. These parameters would only be effective if--mergepairs_strategy consensus is set.
• #807 - Export of TreeSummarizedExperiment R object by default, can be omitted with--skip_tse, also added ability to skip phyloseq R object generation with--skip_phyloseq
• #833 - Add paths to updated version of SBDI-GTDB database.
• #849 - Added Greengenes version 2024.09 of DADA2 taxonomy database:greengenes2=2024.09 orgreengenes2 as parameter to--dada2_ref_taxonomy
• #853 - Added Greengenes2 version 2024.09 for taxonomic classification with QIIME2:greengenes2=2024.09 orgreengenes2 as parameter to--qiime_ref_taxonomy
• #864 - Taxonomic assignment using DADA2 is done in chunks of 10,000 ASVs by default, the chunk size can be adjusted with--dada_assign_chunksize

Changed

• #803 - Changed DADA2_DENOISING :--concatenate_reads renaming to--mergepairs_strategy ; support new method named "consensus" by setting--mergepairs_strategy consensus ; changed options of--mergepairs_strategy from TRUE/FALSE (boolean) to ["merge", "concatenate", "consensus"].
• #818 - Provide users the ability to not bump stack size in vsearch clustering.

Fixed

• #837 - Replaced zenodo.org/record to zenodo.org/records in ref_databases.config to reduce DB download failures
• #800 - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF
• #808 - Add missing library declaration in R script.
• #847 - update theusage.md about sample id format (no dashes allowed)
• #832,#848 - Add pattern to input fields
• #845 - Template update for nf-core/tools version 3.2.0
• #846 - Validation of sample sheet doesnt allow intergers for sampleID any more
• #854,#858 - QIIME2 and Sidle are now also available with conda/mamba
• #862 - ITSx serves now as filter of the abundance table

Dependencies

• #797 - Update QIIME2
• #845 - Update FASTQC module (no version change though) and MultiQC

Removed

• #860 - Removed unused test profiletest_its_dada_taxonomy.

nf-core/ampliseq version 2.12.0 - 2024-11-15

Summary of changes

• updated some reference databases
• several bug fixes
• updated to nf-core template 3.0.2
• dependency updates

Detailed changes

Added

• #786 - Added version 20240904 of Kraken2 standard taxonomy database:standard=20240904 orstandard as parameter to--kraken2_ref_taxonomy

Changed

• #785 - replacedhttps://data.ace.uq.edu.au/public/gtdb/data byhttps://data.gtdb.ecogenomic.org for GTDB versions via--dada_ref_taxonomy

Fixed

• #785,#795 - Template update for nf-core/tools version 3.0.2
• #786 - Creation of the summary report was failing with--dada_ref_taxonomy silva=132
• #792 - Remove white spaces in process tags to avoid errors on some systems

Dependencies

• #785 - Update MultiQC
• #793 - Update Picrust2 and nf-core modules

nf-core/ampliseq version 2.11.0 - 2024-08-06

Summary of changes

This update is mostly about reference taxonomy databases:

• added reference databasessbdi-gtdb=R09-RS220-1 for DADA2
• added reference databasesunite-fungi=10.0 andunite-alleuk=10.0 for SINTAX
• disabled UNITE reference databases for QIIME2
• fixed broken urls for UNITE databases

Detailed changes

Added

• #765 - Added version R09-RS220 of curated GTDB 16S taxonomy:sbdi-gtdb=R09-RS220-1 orsbdi-gtdb as parameter to--dada_ref_taxonomy
• #766 - Added version 10 of Unite as parameter for--sintax_ref_taxonomy:unite-fungi=10.0 andunite-alleuk=10.0

Changed

• #762 - Improved output documentation section "Optional ASV filtering" and parameter documentation
• #766 - Modified warning filenames fromQIIME2_ANCOM to avoid collisions
• #766,#769 - Disabled Unite databases from the--qiime_ref_taxonomy because of divergent results compared to the other classifiers

Fixed

• #761 - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0
• #766 - Fixed broken urls for Unite databases (issue#764)
• #769 - Reference taxonomy database values were not properly validated in versions 2.9.0 and 2.10.0

nf-core/ampliseq version 2.10.0 - 2024-06-27

Summary of changes

• added ANCOM-BC for differential abundance analysis
• updated reference databases forsbdi-gtdb &gtdb withR08-RS214-1 andR09-RS220, respectively
• template update 2.13.1 to 2.14.1
• several bug fixes

Detailed changes

Added

• #751 - Added version R08-RS214 of curated GTDB 16S taxonomy:sbdi-gtdb=R08-RS214-1 orsbdi-gtdb as parameter to--dada_ref_taxonomy
• #752 - Added version R09-RS220 of GTDB 16S taxonomy:gtdb=R09-RS220 orgtdb as parameter to--dada_ref_taxonomy
• #753,#756,#757 - ANCOM-BC via QIIME2 can be used with--ancombc,--ancombc_formula, and--ancombc_formula_reflvl, plotting can be modified with thresholds--ancombc_effect_size and--ancombc_significance

Changed

• #749 - Create barplot also when no metadata is given
• #753 - ANCOM via QIIME2 is not run anymore by default but on request whith--ancom, therefore--skip_ancom was removed

Fixed

• #747 - Template update for nf-core/tools version 2.14.1
• #748 - Updating misleading error message and documentation
• #750 - Numbers inoverall_summary.tsv were fixed (sometimes misleading in 2.9.0 for columns "denoised[F/R]", "merged", and "nochim")

Removed

• #753 ---skip_ancom was removed

nf-core/ampliseq version 2.9.0 - 2024-04-03

Summary of changes

• added multiple regions analysis (including 5R / SMURF / q2-sidle), integratingpipesidle and its software container with1 &2.
• template update 2.11 to 2.13.1
• several bug fixes

Detailed changes

Added

• #700 - Optional--save_intermediates to publish QIIME2 data objects (.qza) and visualisation objects (.qzv)
• #702,#723,#728,#729 - Add multiple regions analysis (including 5R / SMURF / q2-sidle)

Changed

• #719 - Versions of all (instead of selected) processes are now exported topipeline_info/software_versions.yml

Fixed

• #697,#699,#713 - Template update for nf-core/tools version 2.13.1
• #711 - From r207 and onwards Archaea sequences were omitted when parsing GTDB databases. (This did not affectsbdi-gtdb databases, onlygtdb.)
• #715 - Fix filtering vsearch clusters for high number of clusters
• #717 - Fix edge case for sorting file names by using radix method
• #718 - Require a minimum sequence length of 50bp for taxonomic classifcation after using ITSx
• #721 - Fix errorunknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException caused by a missing\ in nf-core modulepigz/uncompress (which had no consequences but was confusing)
• #722 - When barrnap detects several genes select the lowest e-value
• #726 - Add fallback todownload_pipeline.yml because the pipeline does not support stub runs (#2846)

Dependencies

• #720 - Updated nf-core modules, DADA2, and Phyloseq

Removed

• #710 - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0

nf-core/ampliseq version 2.8.0 - 2024-01-16

Summary of changes

• Three additional reference databases available:--qiime_ref_taxonomy greengenes2 (prokaryotic 16S),--dada_ref_taxonomy phytoref (eukaryotic plastid 16S rRNA),--dada_ref_taxonomy zehr-nifh (Nitrogenase iron protein NifH)
• New parameters--qiime_ref_tax_custom,--skip_qiime_downstream,--dada_taxonomy_rc, and--dada_addspecies_allowmultiple
• Bug fixes for using phyloseq, VSEARCH, and error messages
• Updated documentation & reporting
• Pipeline template update

Detailed changes

Added

• #666 - Added Greengenes2 database, version 2022.10, support for QIIME2 taxonomic classification.
• #667,#691 - Added--qiime_ref_tax_custom to permit custom reference database for QIIME2 taxonomic classification
• #674 - Add PhytoRef database for DADA2 taxonomy assignment using--dada_ref_taxonomy phytoref
• #675 - Add the Zehr lab nifH database for DADA2 taxonomy assignment using--dada_ref_taxonomy zehr-nifh
• #681 - For DADA2, with--dada_addspecies_allowmultiple multiple exact species matches are reported and with--dada_taxonomy_rc reverse-complement matches are also considered in taxonomic classification

Changed

• #677 - Added cut_its information to SDBI export

Fixed

• #672,#688,#691 - Updated documentation
• #676 - Phyloseq sometimes only produced one of multiple output files
• #679 - Prevent masking low complexity regions by VSEARCH with lower case letters
• #680,#673 - Improved pipeline summary report & error messages
• #683 - Template update for nf-core/tools version 2.11
• #687 - Correct conda package for ASV SSU filtering

nf-core/ampliseq version 2.7.1 - 2023-11-13

Summary of changes

Downstream analysis with QIIME2 fails on some system with the most recent version of nextflow (23.10.0), this release fixes the issue.

Detailed changes

Changed

• #657 - Improved parameter descriptions and sequence

Fixed

• #655 - AddedNUMBA_CACHE_DIR to fix downstream analysis with QIIME2 that failed on some systems
• #656 - Moved conda-check to script-section and replacedexit 1 witherror()
• #657 - Corrected inaccurate reporting of QIIME2 taxonomic classifications and ASV length filtering

nf-core/ampliseq version 2.7.0 - 2023-10-20

Summary of changes

• Added Pipeline RMarkdown summary report
• Added optional ASV to OTU post-clustering with VSEARCH
• Added Kraken2 as another optional taxonomic classification tool
• Splitted--input into 3 parameters,--input now points to a sampleheet, alternatives are--input_fasta &--input_folder to accommodate nf-validation'sfromSamplesheet
• Update to nf-core template to 2.10

Detailed changes

Added

• #558,#619,#625,#632,#644 - Pipeline summary report
• #615 - Phyloseq R object creation
• #622 - ASV post-clustering with Vsearch
• #637 - Taxonomic classification with Kraken2, parameter--kraken2_ref_taxonomy,--kraken2_ref_tax_custom,--kraken2_assign_taxlevels,--kraken2_confidence
• #639 - GTDB release 214.1 for taxonomic classification with DADA2, using--dada_ref_taxonomy gtdb or--dada_ref_taxonomy gtdb=R08-RS214
• #641 - Continue analysis even when individual files fail the filtering threshold, added parameter--ignore_failed_filtering

Changed

• #616 - When using a sample sheet with--input containing forward and reverse reads, specifying--single_end will only extract forward reads and treat the data as single ended instead of extracting forward and reverse reads.
• #616 ---input was split into three params: (1)--input for samplesheet, (2)--input_fasta for ASV/OTU fasta input, (3)--input_folder direct FASTQ input

• #639 ---dada_ref_taxonomy gtdb points towards GTDB release 214.1 instead of GTDB release 207 for taxonomic classification with DADA2
• #645 - Updated documentation, including workflow figure

Fixed

• #605 - Make--sbdiexport compatible with PR2 version 5.0.0
• #614,#620,#642 - Template update for nf-core/tools version 2.10
• #617 - Fix database compatibility check for--sbdiexport
• #628 - Fix edge case for sample sheet input when using specific combinations of sampleID and forwardReads or reverseReads that will forward one file too much to cutadapt
• #630 - ASV rRNA (barrnap), length, and codon filter now work with ASV fasta file input
• #633 - UNIFRAC in QIIME2_DIVERSITY_CORE is now prevented from using a GPU to avoid errors
• #643 - Fix using--skip_dada_addspecies without--dada_ref_tax_custom_sp which was broken in 2.6.0 & 2.6.1
• #647 - Update of credits

Dependencies

• #646 - Updated dependencies, see below:

nf-core/ampliseq version 2.6.1 - 2023-06-28

Summary of changes

This release fixes a bug with container registry.

Detailed changes

Fixed

• #603 - Fix all containers registry