Releases: nf-core/ampliseq
Releases · nf-core/ampliseq
Ampliseq Version 2.14.0
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
- Updated
sbdi-gtdb, gtdb, PR2 databases and added BOLD plant databases for classification with DADA2
- Follow nextflow's strict syntax (only impacts development)
Detailed changes
Added
- #879 - Add
sbdi-gtdb=R10-RS226-1 as parameter to --dada_ref_taxonomy and make this version the default for sbdi-gtdb.
- #882 - Add
gtdb=R10-RS226 as parameter to --dada_ref_taxonomy and make this version the default for gtdb.
- #883 - Add BOLD databases
plantae-bold-its1 & plantae-bold-trnL, for plant samples with markers ITS1 and trnL, versions 20240510, for DADA2 as parameter to --dada2_ref_taxonomy.
- #885 - Add
pr2=5.1.0 as parameter to --dada_ref_taxonomy and make this version the default for pr2.
Changed
- #871 - Multi-region analysis is now easier with custom databases. No alignment file of the reference sequences are needed.
| Parameter |
Description |
| sidle_ref_tax_custom |
Changed: Previously three files, now one file: path to reference taxonomy strings |
| sidle_ref_seq_custom |
New: Path to reference taxonomy sequences in fasta format |
| sidle_ref_aln_custom |
New: Path to multiple sequence alignment of reference taxonomy sequences in fasta format |
| sidle_ref_degenerates |
New: Only effective with --sidle_ref_tax_custom, filter reference sequences, default: 5 |
| sidle_ref_cleaning |
New: Arguments regarding ad-hoc cleaning, with --sidle_ref_tax_custom default is '--p-database silva' |
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
Ampliseq Version 2.13.0
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 or silva as parameter to --dada2_ref_taxonomy
- #801 - Parameter
--quality_type allows specifying the type of quality scores in raw read data, by default Auto (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 or greengenes2 as parameter to --dada2_ref_taxonomy
- #853 - Added Greengenes2 version 2024.09 for taxonomic classification with QIIME2:
greengenes2=2024.09 or greengenes2 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
| New parameter |
Description |
Default Value |
| quality_type |
Set the input data quality type for DADA2 |
"Auto" |
| mergepairs_strategy |
Choose the method of pair end merging strategy |
"merge" |
| mergepairs_consensus_match |
The score assigned for each matching base pair during sequence alignment. |
1 |
| mergepairs_consensus_mismatch |
The penalty score assigned for each mismatched base pair during sequence alignment. |
-2 |
| mergepairs_consensus_gap |
The penalty score assigned for each gap introduced during sequence alignment. |
-4 |
| mergepairs_consensus_minoverlap |
The minimum number of overlapping base pairs required to merge forward and reverse reads. |
12 |
| mergepairs_consensus_maxmismatch |
The maximum number of mismatches allowed within the overlapping region for merging reads. |
0 |
| mergepairs_consensus_percentile_cutoff |
The percentile cutoff determining the minimum observed overlap in the dataset. |
0.001 |
| skip_tse |
Skip generation of a TreeSummarizedExperiment R object |
false |
| skip_phyloseq |
Skip generation of a Phyloseq R object |
false |
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 the
usage.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
| software |
previously |
now |
| QIIME2 |
2023.7 |
2024.10 |
| MultiQC |
1.25.1 |
1.27 |
Removed
- #860 - Removed unused test profile
test_its_dada_taxonomy.
Ampliseq Version 2.12.0
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 or standard as parameter to --kraken2_ref_taxonomy
Changed
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
| software |
previously |
now |
| MultiQC |
1.21 |
1.25.1 |
| Kraken2 |
2.1.2 |
2.1.3 |
| Picrust2 |
2.5.2 |
2.5.3 |
Ampliseq Version 2.11.0
nf-core/ampliseq version 2.11.0 - 2024-08-06
Summary of changes
This update is mostly about reference taxonomy databases:
- added reference databases
sbdi-gtdb=R09-RS220-1 for DADA2
- added reference databases
unite-fungi=10.0 and unite-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 or sbdi-gtdb as parameter to --dada_ref_taxonomy
- #766 - Added version 10 of Unite as parameter for
--sintax_ref_taxonomy: unite-fungi=10.0 and unite-alleuk=10.0
Changed
- #762 - Improved output documentation section "Optional ASV filtering" and parameter documentation
- #766 - Modified warning filenames from
QIIME2_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
Ampliseq Version 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 for
sbdi-gtdb & gtdb with R08-RS214-1 and R09-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 or sbdi-gtdb as parameter to --dada_ref_taxonomy
- #752 - Added version R09-RS220 of GTDB 16S taxonomy:
gtdb=R09-RS220 or gtdb 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 in
overall_summary.tsv were fixed (sometimes misleading in 2.9.0 for columns "denoised[F/R]", "merged", and "nochim")
Removed
- #753 -
--skip_ancom was removed
Ampliseq Version 2.9.0
nf-core/ampliseq version 2.9.0 - 2024-04-03
Summary of changes
- added multiple regions analysis (including 5R / SMURF / q2-sidle), integrating pipesidle and its software container with 1 & 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 to
pipeline_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 affect
sbdi-gtdb databases, only gtdb.)
- #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 error
unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException caused by a missing \ in nf-core module pigz/uncompress (which had no consequences but was confusing)
- #722 - When barrnap detects several genes select the lowest e-value
- #726 - Add fallback to
download_pipeline.yml because the pipeline does not support stub runs (#2846)
Dependencies
- #720 - Updated nf-core modules, DADA2, and Phyloseq
| software |
previously |
now |
| cutadapt |
3.4 |
4.6 |
| DADA2 |
1.28.0 |
1.30.0 |
| Phyloseq |
1.44.0 |
1.46.0 |
Removed
- #710 - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0
Ampliseq Version 2.8.0
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
Ampliseq Version 2.7.1
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 - Added
NUMBA_CACHE_DIR to fix downstream analysis with QIIME2 that failed on some systems
- #656 - Moved conda-check to script-section and replaced
exit 1 with error()
- #657 - Corrected inaccurate reporting of QIIME2 taxonomic classifications and ASV length filtering
Ampliseq Version 2.7.0
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's fromSamplesheet
- 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
| Param updated |
Param old |
Accepts |
| input |
input |
samplesheet, .tsv/.csv/.yml/.yaml |
| input_fasta |
input |
ASV/OTU sequences, .fasta |
| input_folder |
input |
Folder containing compressed fastq files |
- #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:
| software |
previously |
now |
| FASTQC |
0.11.9 |
0.12.1 |
| DADA2 |
1.22.0 |
1.28.0 |
| PICRUSt2 |
2.5.0 |
2.5.2 |
| QIIME2 |
2022.11 |
2023.7 |
Ampliseq Version 2.6.1
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
