Version history
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
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_VERlatest-everything
& pull_request tomaster
tests with NXF_VER22.10.1
&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)
toNextflow.error()
- #594 - Update metadata documentation
- #595 - Closing gaps in rarefaction depth for diversity calculations (
mindepth
in QIIME2_DIVERSITY_CORE)
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
.
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 |
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
andmidori2-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 |
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
nf-core/ampliseq version 2.3.1 - 2022-04-05
Summary of changes
This release fixes a bug.
Detailed changes
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.
nf-core/ampliseq version 2.3.0 - 2022-04-04
Summary of changes
- Added Barrnap that annotates whether ASV sequences are SSUs and filter on demand
- Primer sequences are now not required any more and cutadapt can be skipped
- Updated to nf-core template 2.3.2
- Fixed some bugs
Detailed changes
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. - #395 -
--seed
specifies the random seed. - #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.
- #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.
Dependencies
Tool | Previous version | New version |
---|---|---|
MultiQC | 1.11 | 1.12 |
nf-core/ampliseq version 2.2.0 - 2022-01-31
Summary of changes
- Added features (e.g. SBDI-GTDB db update, Adonis test)
- Added convenience updates (e.g. properly reporting and on demand ignoring low read samples)
- Updated to nf-core template 2.2
- Fixed some bugs
Detailed changes
Added
- #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
Summary of changes
This release fixes bugs.
Detailed changes
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. - 342 - Added PICRUSt2 to summary figure.
Fixed
nf-core/ampliseq version 2.1.0 “Gray Steel Boa” - 2021-09-14
Summary of changes
- Updated documentation
- Added export to the Swedish Biodiversity Infrastructure (SBDI) on demand (
--sbdiexport
) - Added newer versions of reference databases
- Predict community functions on demand (
--picrust
) for 16S rRNA amplicons with PICRUSt2 - Fixed some bugs
Detailed changes
Added
- #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-gtdb
as parameter to--dada_ref_taxonomy
- #318 - Output information about the used reference taxonomy in a separate file in results folder
dada2/
orqiime2/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) - #305 -
--max_len
now accepts integers as expected - #314, #315 - ASV fasta input via —input fixed (was broken in 2.0.0) and a test profile was added.
Dependencies
nf-core/ampliseq version 2.0.0 “Blue Copper Kangaroo” - 2021-06-29
Summary of changes
- Re-wrote whole pipeline in nextflow DSL2 instead of DSL1
- Three types of input is now supported: data folder, sample sheet, ASV fasta file
- ASV generation is now performed by DADA2 in R instead of DADA2 in QIIME2
- More reference taxonomy databases are now supported out of the box (SILVA, UNITE, PR2, GTDB, RDP)
- More data types can be analysed (Illumina SE & PE, PacBio, IonTorrent)
Detailed changes
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 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_qiime
to prevent any steps that are executed with QIIME2 - #272 -
--cut_its
to cut ASV sequence to ITS region before performing taxonomic classification with DADA2 - #280 - Added support for IonTorrent data
- #283 -
--cut_dada_ref_taxonomy
allows extracting expected amplicons from DADA2 reference taxonomy database
Changed
- #254 - Updated CamelCase parameters to be lower_case_snake_case:
multipleSequencingRuns
tomultiple_sequencing_runs
minLen
tomin_len
maxLen
tomax_len
maxEE
tomax_ee
- #277 - Requires nextflow version
>= 21.04.0
Fixed
- #273 - Template update for nf-core/tools version 1.14
Dependencies
- #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
Removed
- #229 -
--manifest
is superseeded by--input
that can now also handle a sample sheet file input (required extension:.tsv
) - #229 -
--Q2imported
anduntilQ2import
are removed because pausing at that point is not neccessary - #229 -
--split
is no longer supported, therefore all sample IDs have to be unique - #229 -
--classifier_removeHash
and--qiime_timezone
became unnecessary - #229 -
--onlyDenoising
is deprecated in favour of--skip_taxonomy
(which does the exact same thing) --taxon_reference
became unnecessary- #229 -
--reference_database
and--dereplication
are not supported any more.--qiime_ref_taxonomy
allows now choosing a taxonomic reference
nf-core/ampliseq version 1.2.0 “Teal Bronze Lion” - 2021
Added
- #106 - Added support for PacBio data
- Added
--taxon_reference
to be able to support both ‘silva’ and ‘unite’ - #157 - Added possibility to run double cutadapt steps,
--double_primer
- #211 - Added quality filter option
--maxEE
Fixed
- #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_classifier
in 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
Dependencies
- Updated from cutadapt v2.6 to v2.8
nf-core/ampliseq version 1.1.3 - 2020
Added
- #170 - Cite paper for initial release
- #111 - Added parameter for user specified manifest file
- #118 - Added social preview images
- #135 - Added
--trunc_rmin
to make sure that auto trunc cutoff retaines a certain fraction of reads
Fixed
- #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
Dependencies
- Updated from MultiQC v1.6 to v1.9
Deprecated
--reads
is replaced by--input
due to nf-core/tools v1.10.2
nf-core/ampliseq version 1.1.2 - 2019
- No further changes, except a bugfix for the timezone issue found by @marchoeppner
- Specification of ‘—qiime_timezone’ might be required to run the analysis appropriately
nf-core/ampliseq version 1.1.1 - 2019
Pipeline Updates
- Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10
Bugfixes
- #78 - All sequenced classified to the same species
nf-core/ampliseq version 1.1.0 “Silver Lime Bee” - 2019
Pipeline updates
- #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
Bug fixes
Initial release of nfcore/ampliseq!
The pipeline is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.
The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa (ANCOM). See the output documentation for more details of the results.