The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #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.
- #444 - Updated parameter documentation.
- #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_categoryinstead of ignoring that setting. - #451 - Replace busybox with Ubuntu base image for GCP support.
- #429 -
--cutadapt_min_overlapsets cutadapt's global minimum overlap (-O) and--cutadapt_max_error_ratesets cutadapt's global maximum error rate (-e) for trimming primer sequences. - #431 -
--skip_dada_qualityallows to skip quality check with DADA2. This is only allowed when--trunclenfand--trunclenrare set. - #434 -
--addshadds UNITE species hypothesis (SH) to the taxonomy. Only available for UNITE databases.
- #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
--trunlenfand--trunclenr. This should make the process more robust also from larger data sets.
- #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
- #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_formulais required to run that step.
- #385 -
--skip_cutadaptallows 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. - #395 -
--seedspecifies the random seed. - #396 - Barrnap annotates ASV sequences for SSU's, it can be skipped with
--skip_barrnap.--filter_ssutakes 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).
- #385 -
--FW_primerand--RV_primerare 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).
- #384 - For QIIME2 beta diversity, make directory before execution.
- #394 - Prevent simultaneous usage of
--qiime_ref_taxonomyand--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.
- #405 - Fix omitting taxonomic filtering (QIIME2_FILTERTAXA).
- #404 - Rephrase error message for empty input files and empty files after trimming with cutadapt.
- #407 - Fix reformatting script for Unite.
| Tool | Previous version | New version |
|---|---|---|
| MultiQC | 1.11 | 1.12 |
- #352, #372 -
--skip_dada_addspeciesallows to skip species level classification to reduce memory requirements, incompatible with--sbdiexportthat expect species annotation. - #364 - Adonis in QIIME2 for testing feature importance in beta diversity distances,
--qiime_adonis_formulacan 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.)
- #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_filesor--ignore_failed_trimming, respectively. - #376 - Forbid sampleIDs starting with a number when also
--metadatais used, because such strings are unintentionally modified and the metadata will not match any more.
- #377- An error message will occur when
--sbdiexportis used with--skip_taxonomyor--skip_dada_addspecies - #375- Updated documentation regarding not using curly brackets in
--extensionwith--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
| 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 |
- #350 - Remove redundant derepFastq step (has no impact on results)
- #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
- 338 - Write empty space instead of
NAfor missing values in output files. - 342 - Added PICRUSt2 to summary figure.
- #329 - Improve error message when no data files are found
- #330 - Make
--skip_fastqcusable again - #339 - Fix sample names when using
--double_primeror--illumina_pe_its
- #322 - Export to the Swedish Biodiversity Infrastructure (SBDI)
- #294 - New version of the PR2 taxonomy database: 4.14.0, contains also some Bacteria, see PR2 release 4.14.0 notes
- #294 - New version of the Unite taxonomy databases: 8.3
- #302 - Pipeline workflow figure in README.md
- #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-gtdbas parameter to--dada_ref_taxonomy - #318 - Output information about the used reference taxonomy in a separate file in results folder
dada2/orqiime2/taxonomy
- #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.
- #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_primerin usual direction (before: reverse complement) - #305 -
--max_lennow accepts integers as expected - #314, #315 - ASV fasta input via --input fixed (was broken in 2.0.0) and a test profile was added.
Re-wrote whole pipeline in nextflow DSL2 instead of DSL1
- #229 -
--single_endfor single-ended Illumina data - #229, #245, #267 - Taxonomic classification with DADA2
- #229 -
--dada_ref_taxonomyfor taxonomic classification with DADA2's assignTaxonomy and addSpecies functions - #278 -
--qiime_ref_taxonomyfor taxonomic classification with QIIME2 - #239 - Support of RDP database for DADA2 classification
- #237 - Support of UNITE database for DADA2 classification
- #229 -
--inputmay point (1) at a fasta file ending with.fasta/.fna/.fathat will be taxonomically classified, (2) at a samples sheet ending with.tsvthat allows analysis of multiple sequencing runs by reading the optional columnrun, or (3) at a folder input - #229 -
--sample_inference,--concatenate_reads,--illumina_pe_its; please check the documentation for their function - #275 - Read count summary
- #274 -
--skip_qiimeto prevent any steps that are executed with QIIME2 - #272 -
--cut_itsto cut ASV sequence to ITS region before performing taxonomic classification with DADA2 - #280 - Added support for IonTorrent data
- #283 -
--cut_dada_ref_taxonomyallows extracting expected amplicons from DADA2 reference taxonomy database
- #254 - Updated CamelCase parameters to be lower_case_snake_case:
multipleSequencingRunstomultiple_sequencing_runsminLentomin_lenmaxLentomax_lenmaxEEtomax_ee
- #277 - Requires nextflow version
>= 21.04.0
- #273 - Template update for nf-core/tools version 1.14
- #272 - New dependency ITSx v1.1.3
- #229 - Updated from cutadapt v2.8 to v3.2
- #229 - Updated DADA2 from v1.10 to v1.18.0, now not using QIIME2 for ASV generation any more
- #229 - Updated QIIME2 to v2021.2
- #229 -
--manifestis superseeded by--inputthat can now also handle a sample sheet file input (required extension:.tsv) - #229 -
--Q2importedanduntilQ2importare removed because pausing at that point is not neccessary - #229 -
--splitis no longer supported, therefore all sample IDs have to be unique - #229 -
--classifier_removeHashand--qiime_timezonebecame unnecessary - #229 -
--onlyDenoisingis deprecated in favour of--skip_taxonomy(which does the exact same thing) --taxon_referencebecame unnecessary- #229 -
--reference_databaseand--dereplicationare not supported any more.--qiime_ref_taxonomyallows now choosing a taxonomic reference
- #106 - Added support for PacBio data
- Added
--taxon_referenceto be able to support both 'silva' and 'unite' - #157 - Added possibility to run double cutadapt steps,
--double_primer - #211 - Added quality filter option
--maxEE
- #182 - Fix input in case there are no underscores in sample IDs
- #186 - Update github actions
- #187 - Sample ids are in incorrect order in feature-table from PacBio data
- #201 - Template update for nf-core/tools version 1.12.1
- #147 - Split
make_classifierin two different processes that can be allocated different resources - #183 - Don't fetch taxonomy/create classifier when run with
--skip_taxonomy - #180 - MultiQC, cutadapt and fastQC now work with
--multipleSequencingRuns
- Updated from cutadapt v2.6 to v2.8
- #170 - Cite paper for initial release
- #111 - Added parameter for user specified manifest file
- #118 - Added social preview images
- #135 - Added
--trunc_rminto make sure that auto trunc cutoff retaines a certain fraction of reads
- #172 - Template update for nf-core/tools v1.11
- #163 - Template update for nf-core/tools v1.10.2
- #136 - Pipeline fails with remote working directory
- #152 - Don't fetch taxonomy/create classifier when run with
--onlyDenoising
- Updated from MultiQC v1.6 to v1.9
--readsis replaced by--inputdue to nf-core/tools v1.10.2
- No further changes, except a bugfix for the timezone issue found by @marchoeppner
- Specification of
--qiime_timezonemight be required to run the analysis appropriately
- Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10
- Export absolute abundance files into 'results/abundance-table/filtered/' for optional external secondary analysis
- #78 - All sequenced classifed to the same species
- #40 - Added support for data originating from multiple sequencing runs
- #53 - DADA2 report is always exported
- #49 - Allowed more filtering options
- #5 - Introduced check for existence of input files
- Extended parameter sanity check, including #15
- #61 - Improved documentation
- #62 - Utilize nf-core/configs centrally for this pipeline
- #63 - QIIME imports files by using a manifest, giving more freedom with input file names
- #84 - Add proper nf-core logo
Initial release of nf-core/ampliseq, created with the nf-core template.