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

• #528 - Updated QIIME2

Tool	Previous version	New version
QIIME2	2022.8	2022.11

Removed

• #513 - Removed parameter --enable_conda.

Ampliseq Version 2.4.1

nf-core/ampliseq version 2.4.1 - 2022-12-07

Summary of changes

Most importantly this release fixes a bug in 2.4.0 that prevented the use of the SILVA v138 database with QIIME2.

Detailed changes

Added

• #494 - --metadata_category_barplot accepts a comma separated list of metadata categories and plots for each barplots with average relative abundance.

Changed

• #492 - --qiime_adonis_formula accepts a comma separated list of formulas.

Fixed

• #486 - Fixed typo in error message stating --skip_classifer instead of --classifier.
• #487,#488 - Update stale links in usage documentation.
• #489 - Reduce linting warnings for nf-core tools version 2.5.1.
• #491 - Make output from --addSH match UNITE format by replacing spaces with underscores.
• #495 - Template update for nf-core/tools version 2.6
• #501 - Check for empty fields in samplesheet column "run" and raise an appropriate error.
• #503 - Changed environment for formatting databases.
• #504 - Fixed warnings with nextflow 22.10 (and later) about processes that are defined more than once.

Dependencies

Tool	Previous version	New version
QIIME2	2021.8	2022.8