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#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
Dependencies
Removed
nf-core/ampliseq version 2.10.0 - 2024-06-27
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")
#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
nf-core/ampliseq version 2.8.0 - 2024-01-16
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
#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
#575, #586 - Added filtering step for stop codons for ASVs that are of coding regions.
#597 - Samples with less reads than specified with --min_read_counts (default: 1) stop the pipeline, previously the threshold was 1KB in size.
Changed
#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
#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
#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.".
#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
#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
Removed
nf-core/ampliseq version 2.4.0 - 2022-09-07
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.
#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
#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.
#434 - --addsh adds UNITE species hypothesis (SH) to the taxonomy. Only available for UNITE databases.
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
Dependencies
Removed
nf-core/ampliseq version 2.3.1 - 2022-04-05
Added
Changed
Fixed
#415 - ADONIS test was running by default in version 2.2.0 and 2.3.0 on metadata columns that did not always have the required format, now specifying --qiime_adonis_formula is required to run that step.
Dependencies
Removed
nf-core/ampliseq version 2.3.0 - 2022-04-04
Added
#385 - --skip_cutadapt allows to skip primer trimmimg.
#390, #408 - Add values to option --cut_its, specifying which ITS part to use. Also, add option --its_partial <x> to allow partial ITS sequences longer than given cutoff.
#396 - Barrnap annotates ASV sequences for SSU's, it can be skipped with --skip_barrnap. --filter_ssu takes a comma separated list of "bac,arc,mito,euk" and enables SSU filtering depending on Barrnap (default: off).
#397 - Complement README.md with links to the nf-core bytesize 25 (nf-core/ampliseq).
Changed
#385 - --FW_primer and --RV_primer are not obligatory any more, however primer sequences are still required with cutadapt (i.e. without --skip_cutadapt), --qiime_ref_taxonomy, and --cut_dada_ref_taxonomy (cuts reference with primer sequences).
Fixed
#384 - For QIIME2 beta diversity, make directory before execution.
#394 - Prevent simultaneous usage of --qiime_ref_taxonomy and --classifier.
#402, #410 - Template update for nf-core/tools version 2.3.2
#403 - Limit number of files for DADA2_QUALITY (plotQualityProfile) by read numbers.
#352, #372 - --skip_dada_addspecies allows to skip species level classification to reduce memory requirements, incompatible with --sbdiexport that expect species annotation.
#364 - Adonis in QIIME2 for testing feature importance in beta diversity distances, --qiime_adonis_formula can be set to provide a custom formula.
#366 - New version of the SBDI-GTDB taxonomy database: v. 3. (Fixes problem with Reverse_ added to some domain strings.)
Changed
#354 - Input files and files after primer trimming with cutadapt are required to be >1KB (i.e. not empty) and either the pipeline will stop if at least one sample file fails or the failing samples will be ignored when using --ignore_empty_input_files or --ignore_failed_trimming, respectively.
#376 - Forbid sampleIDs starting with a number when also --metadata is used, because such strings are unintentionally modified and the metadata will not match any more.
Fixed
#377- An error message will occur when --sbdiexport is used with --skip_taxonomy or --skip_dada_addspecies
#375- Updated documentation regarding not using curly brackets in --extension with --single_end
#362- Template update for nf-core/tools version 2.2, now requires nextflow version >= 21.10.3
#374- Cutadapt results can be now also viwed in the MultiQC report
Dependencies
Tool
Previous version
New version
Cutadapt
3.2
3.4
DADA2
1.20.0
1.22.0
QIIME2
2021.2
2021.8
PICRUSt2
2.4.1
2.4.2
MultiQC
1.10.1
1.11
Removed
#350 - Remove redundant derepFastq step (has no impact on results)
nf-core/ampliseq version 2.1.1 - 2021-10-28
Added
#336 - Taxa agglomeration levels with --dada_tax_agglom_min, --dada_tax_agglom_max, --qiime_tax_agglom_min, --qiime_tax_agglom_max, with defaults that go to genus level for abundance tables and ANCOM analysis
Changed
338 - Write empty space instead of NA for missing values in output files.
#307 - Functional predictions with PICRUSt2, on demand with --picrust
#310 - Workflow figure in usage.md when using --multiple_sequencing_runs
#312 - Added curated GTDB 16S taxonomy: sbdi-gtdb as parameter to --dada_ref_taxonomy
#318 - Output information about the used reference taxonomy in a separate file in results folder dada2/ or qiime2/taxonomy
Changed
#313 - Relative abundance tables in qiime2/rel_abundance_tables/ on ASV level were renamed and with either DADA2 (rel-table-ASV_with-DADA2-tax.tsv) or QIIME2 classifications (rel-table-ASV_with-QIIME2-tax.tsv), if available.
Fixed
#306 - Sample names can now be identical to basenames of read files
#299, #301- Template update for nf-core/tools version 2.1
#303 - Reverse primer of PacBio and IonTorrent reads should be now given to --RV_primer in usual direction (before: reverse complement)
nf-core/ampliseq version 2.0.0 "Blue Copper Kangaroo" - 2021-06-29
Re-wrote whole pipeline in nextflow DSL2 instead of DSL1
Added
#229 - --single_end for single-ended Illumina data
#229, #245, #267 - Taxonomic classification with DADA2
#229 - --dada_ref_taxonomy for taxonomic classification with DADA2's assignTaxonomy and addSpecies functions
#278 - --qiime_ref_taxonomy for taxonomic classification with QIIME2
#239 - Support of RDP database for DADA2 classification
#237 - Support of UNITE database for DADA2 classification
#229 - --input may point (1) at a fasta file ending with .fasta/.fna/.fa that will be taxonomically classified, (2) at a samples sheet ending with .tsv that allows analysis of multiple sequencing runs by reading the optional column run, or (3) at a folder input
#229 - --sample_inference, --concatenate_reads, --illumina_pe_its; please check the documentation for their function