Releases: nf-core/ampliseq
Releases · nf-core/ampliseq
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
Ampliseq Version 2.6.0
nf-core/ampliseq version 2.6.0 - 2023-06-27
Summary of changes
- Updated taxonomic databases (UNITE 9.0, PR2 5.0.0)
- Added more choice for taxonomic classification: phylogenetic placement, SINTAX
- Codon usage based filtering allows for additional QC of coding regions
- Add NF-TEST pipeline end-to-end tests for existing CI tests
- nf-core template update from 2.7.2 to 2.8
Detailed changes
Added
- #564,#567,#582 - Added phylogenetic placement
- #577 - Added SINTAX for taxonomic classification
- #575, #586 - Added filtering step for stop codons for ASVs that are of coding regions.
- #580 - Add NF-TEST pipeline end-to-end tests for existing CI tests
- #591 - New version of the Unite taxonomy databases: 9.0
- #596 - New version of the PR2 taxonomy database: 5.0.0, only available with DADA2 (
--dada_ref_taxonomy)
- #597 - Samples with less reads than specified with
--min_read_counts (default: 1) stop the pipeline, previously the threshold was 1KB in size.
Changed
- #563 - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
- #567 - Renamed
--dada_tax_agglom_min and --qiime_tax_agglom_min to --tax_agglom_min and --dada_tax_agglom_max and --qiime_tax_agglom_max to --tax_agglom_max
- #580 - GitHub Actions CI - pull_request to
dev tests with NXF_VER latest-everything & pull_request to master tests with NXF_VER 22.10.1 & latest-everything
- #598 - Updated Workflow figure with SINTAX and phylogenetic placement
- #599 - For exact species assignment (DADA2's addSpecies) PR2 taxonomy database (e.g.
--dada_ref_taxonomy pr2) now excludes any taxa that end with " sp.".
Fixed
- #553 - Handle empty barrnap results files
- #554 - Accept taxonomy strings that contain
#,'
- #569 - Make header of overall_summary.tsv consistent between input data types
- #573 - Avoid parser error for single-end data when an empty read file is detected
- #578 - Template update for nf-core/tools version 2.8, including changing
System.exit(1) to Nextflow.error()
- #594 - Update metadata documentation
- #595 - Closing gaps in rarefaction depth for diversity calculations (
mindepth in QIIME2_DIVERSITY_CORE)
Ampliseq Version 2.5.0
nf-core/ampliseq version 2.5.0 - 2023-03-02
Summary of changes
- Added COIDB DADA2 taxonomic database
- Small adjustments to taxonomic classification, ASV filtering by barrnap, fasta input
- sbdi-export works for more taxonomic databases now
- nf-core template update from 2.6 to 2.7.2
Detailed changes
Added
- #518,#534 - Add COIDB DADA2 reference taxonomy database
- #521 - Export svg in addition to pdf files for quality plots from DADA2
- #538 - Parameter
--diversity_rarefaction_depth controls the minimum rarefaction depth for diversity analysis, this allows increasing the rarefaction depth at the cost of excluding low count samples. Parameter --ancom_sample_min_count sets the minimum sample counts to retain a sample for ANCOM analysis.
Changed
- #537 - Update output generated with option sbdi-export
- #541 - Remove adjustments of taxonomic levels for RDP & SILVA & GTDB & UNITE database for DADA2 taxonomic classification, reduced default of
--dada_tax_agglom_max from 7 to 6
- #548 -
--filter_ssu accepted any barrnap hit to a kingdom (domain) (any occurence in resulting gff) to choose an ASV, now only ASVs with the kingdom (domain) that has the lowest evalue are accepted.
Fixed
- #513 - Template update for nf-core/tools version 2.7.2
- #519 - Adding the pipeline reference to the MultiQC report
- #520,#530 - Fix conda packages
- #531,#546 - Update documentation
- #535 - Make sure barrnap runs with fasta input
- #544 - Adding module to fix header in fasta input if needed
Dependencies
| Tool |
Previous version |
New version |
| QIIME2 |
2022.8 |
2022.11 |
Removed
- #513 - Removed parameter
--enable_conda.
