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

Ampliseq Version 2.4.0

nf-core/ampliseq version 2.4.0 - 2022-09-07

Summary of changes

• Custom DADA2 reference taxonomy databases are now supported.
• Illumina NovaSeq data can be correctly processed.
• ASV length filter is available for stricter QC.
• Species classification is now reported in columns "Species" using DADA2's assignTaxonomy function or "Species_exact" using DADA2's addSpecies function, the latter only assigns exact sequence matches.

Detailed changes

Added

• #456 - An optional ASV length filter can be activated using --min_len_asv <int> and/or --max_len_asv <int>.
• #458 - Samplesheet, ASV fasta file, and/or metadata sheet is now exported into <results>/input/
• #459 - MIDORI2 CO1 database with keys midori2-co1=gb250 and midori2-co1 for --dada_ref_taxonomy
• #460 - Taxonomic ranks for DADA2 taxonomic classification can be now adjusted using --dada_assign_taxlevels <comma separated string>.
• #461 - A custom DADA2 reference taxonomy database can now be used with --dada_ref_tax_custom and --dada_ref_tax_custom_sp, typically accompanied by --dada_assign_taxlevels.
• #446,#467 - Binned quality scores from Illumina NovaSeq data can be now corrected with --illumina_novaseq.
• #477 - QC plots of DADA2's plotQualityProfile are now also produced after preprocessing.
• #478 - Added GTDB R07-RS207 DADA2 taxonomy reference databases

Changed

• #444,#457,#463,#465,#466,#469 - Updated the documentation.
• #445 - The minimum number of total bases to use for error rate learning by default is 1e8 (DADA2, learnErrors, nbases). Previously, samples were read in the provided order until enough reads were obtained (DADA2, learnErrors, randomize=FALSE). Now, samples are picked at random from those provided (DADA2, learnError, randomize=TRUE) and a seed is set.
• #453 - Export a few more basic QIIME2 fragments (zipped files) that can be easily imported into the correct QIIME2 version for custom analysis.
• #464 - Reported taxonomic classifications on species level based on DADA2's assignTaxonomy (approximations) is now listed in column "Species" while exact matches based on DADA2's addSpecies are now reported in column "Species_exact".

Fixed

• #448 - Updated SBDI export scripts to include Unite species hypothesis information if available.
• #451 - Pairwise statistics will be now performed on a subset of metadata columns specified with --metadata_category instead of ignoring that setting.
• #451 - Replace busybox with Ubuntu base image for GCP support.
• #455 - Stop with descriptive error when only one of --trunclenf and --trunclenr is given, earlier it was silently ignored.
• #474 - Template update for nf-core/tools version 2.5.1
• #475 - Report software versions for DADA2_TAXONOMY

Dependencies

• #479 - Updated software

Tool	Previous version	New version
PICRUSt2	2.4.2	2.5.0
MultiQC	1.12	1.13a

Ampliseq Version 2.3.2

nf-core/ampliseq version 2.3.2 - 2022-05-27

Summary of changes

This release fixes bugs and adds more options to manipulate cutadapt parameters.

Detailed changes

Added

• #429 - --cutadapt_min_overlap sets cutadapt's global minimum overlap (-O) and --cutadapt_max_error_rate sets cutadapt's global maximum error rate (-e) for trimming primer sequences.
• #431 - --skip_dada_quality allows to skip quality check with DADA2. This is only allowed when --trunclenf and --trunclenr are set.

Changed

• #432 - The number of records to sample from a fastq file was decreased from 5e+06 to 5e+04 for plotQualityProfile (DADA2_QUALITY), therefore a smaller subset of reads is sampled for determining --trunlenf and --trunclenr. This should make the process more robust also from larger data sets.

Fixed

• #428 - Fixed samplesheet sampleID entries, now allows dashes.
• #433 - Fixed typos and improved documentation layout.
• #437 - Template update for nf-core/tools version 2.4
• #439 - Fixed a bug in DADA2_QUALITY process with large number of nucleotides.