# nf-core/ampliseq: Changelog

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## nf-core/ampliseq version 2.3.1 - 2022-04-05

### `Added`

### `Changed`

### `Fixed`

- [#415](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/385) - `--skip_cutadapt` allows to skip primer trimmimg.
- [#390](https://github.com/nf-core/ampliseq/pull/390), [#408](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/395) - `--seed` specifies the random seed.
- [#396](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/397) - Complement README.md with links to the nf-core bytesize 25 (nf-core/ampliseq).

### `Changed`

- [#385](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/384) - For QIIME2 beta diversity, make directory before execution.
- [#394](https://github.com/nf-core/ampliseq/pull/394) - Prevent simultaneous usage of `--qiime_ref_taxonomy` and `--classifier`.
- [#402](https://github.com/nf-core/ampliseq/pull/402), [#410](https://github.com/nf-core/ampliseq/pull/410) - Template update for nf-core/tools version 2.3.2
- [#403](https://github.com/nf-core/ampliseq/pull/403) - Limit number of files for DADA2_QUALITY (plotQualityProfile) by read numbers.
- [#405](https://github.com/nf-core/ampliseq/pull/405) - Fix omitting taxonomic filtering (QIIME2_FILTERTAXA).
- [#404](https://github.com/nf-core/ampliseq/pull/404) - Rephrase error message for empty input files and empty files after trimming with cutadapt.
- [#407](https://github.com/nf-core/ampliseq/pull/407) - Fix reformatting script for Unite.

### `Dependencies`

| Tool    | Previous version | New version |
| ------- | ---------------- | ----------- |
| MultiQC | 1.11             | 1.12        |

### `Removed`

## nf-core/ampliseq version 2.2.0 - 2022-01-31

### `Added`

- [#352](https://github.com/nf-core/ampliseq/pull/352), [#372](https://github.com/nf-core/ampliseq/pull/372) - `--skip_dada_addspecies` allows to skip species level classification to reduce memory requirements, incompatible with `--sbdiexport` that expect species annotation.
- [#364](https://github.com/nf-core/ampliseq/pull/364) - Adonis in QIIME2 for testing feature importance in beta diversity distances, `--qiime_adonis_formula` can be set to provide a custom formula.
- [#366](https://github.com/nf-core/ampliseq/pull/366) - New version of the SBDI-GTDB taxonomy database: v. 3. (Fixes problem with `Reverse_` added to some domain strings.)

### `Changed`

- [#354](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/377)- An error message will occur when `--sbdiexport` is used with `--skip_taxonomy` or `--skip_dada_addspecies`
- [#375](https://github.com/nf-core/ampliseq/pull/375)- Updated documentation regarding not using curly brackets in `--extension` with `--single_end`
- [#362](https://github.com/nf-core/ampliseq/pull/362)- Template update for nf-core/tools version 2.2, now requires nextflow version `>= 21.10.3`
- [#374](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/350) - Remove redundant derepFastq step (has no impact on results)

## nf-core/ampliseq version 2.1.1 - 2021-10-28

### `Added`

- [#336](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/338) - Write empty space instead of `NA` for missing values in output files.
- [342](https://github.com/nf-core/ampliseq/pull/342) - Added PICRUSt2 to summary figure.

### `Fixed`

- [#329](https://github.com/nf-core/ampliseq/issues/329) - Improve error message when no data files are found
- [#330](https://github.com/nf-core/ampliseq/issues/330) - Make `--skip_fastqc` usable again
- [#339](https://github.com/nf-core/ampliseq/issues/339) - Fix sample names when using `--double_primer` or `--illumina_pe_its`

### `Dependencies`

### `Removed`

## nf-core/ampliseq version 2.1.0 "Gray Steel Boa" - 2021-09-14

### `Added`

- [#322](https://github.com/nf-core/ampliseq/pull/322) - Export to the Swedish Biodiversity Infrastructure (SBDI)
- [#294](https://github.com/nf-core/ampliseq/pull/294) - New version of the PR2 taxonomy database: 4.14.0, contains also some Bacteria, see [PR2 release 4.14.0 notes](https://github.com/pr2database/pr2database/releases/tag/v4.14.0)
- [#294](https://github.com/nf-core/ampliseq/pull/294) - New version of the Unite taxonomy databases: 8.3
- [#302](https://github.com/nf-core/ampliseq/pull/302) - Pipeline workflow figure in README.md
- [#307](https://github.com/nf-core/ampliseq/pull/307) - Functional predictions with PICRUSt2, on demand with `--picrust`
- [#310](https://github.com/nf-core/ampliseq/pull/310) - Workflow figure in usage.md when using `--multiple_sequencing_runs`
- [#312](https://github.com/nf-core/ampliseq/pull/312) - Added curated GTDB 16S taxonomy: `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
- [#318](https://github.com/nf-core/ampliseq/pull/318) - Output information about the used reference taxonomy in a separate file in results folder `dada2/` or `qiime2/taxonomy`

### `Changed`

- [#313](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/306) - Sample names can now be identical to basenames of read files
- [#299](https://github.com/nf-core/ampliseq/pull/299), [#301](https://github.com/nf-core/ampliseq/pull/301)- Template update for nf-core/tools version 2.1
- [#303](https://github.com/nf-core/ampliseq/pull/303) - Reverse primer of PacBio and IonTorrent reads should be now given to `--RV_primer` in usual direction (before: reverse complement)
- [#305](https://github.com/nf-core/ampliseq/pull/305) - `--max_len` now accepts integers as expected
- [#314](https://github.com/nf-core/ampliseq/pull/314), [#315](https://github.com/nf-core/ampliseq/pull/315) - ASV fasta input via --input fixed (was broken in 2.0.0) and a test profile was added.

### `Dependencies`

- [#299](https://github.com/nf-core/ampliseq/pull/299) - Updated MultiQC to v1.10
- [#319](https://github.com/nf-core/ampliseq/pull/319) - Updated DADA2 from 1.18.0 to 1.20.0

### `Removed`

## nf-core/ampliseq version 2.0.0 "Blue Copper Kangaroo" - 2021-06-29

Re-wrote whole pipeline in nextflow [DSL2](https://www.nextflow.io/docs/latest/dsl2.html) instead of DSL1

### `Added`

- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--single_end` for single-ended Illumina data
- [#229](https://github.com/nf-core/ampliseq/pull/229), [#245](https://github.com/nf-core/ampliseq/pull/245), [#267](https://github.com/nf-core/ampliseq/pull/267) - Taxonomic classification with DADA2
- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--dada_ref_taxonomy` for taxonomic classification with DADA2's assignTaxonomy and addSpecies functions
- [#278](https://github.com/nf-core/ampliseq/pull/278) - `--qiime_ref_taxonomy` for taxonomic classification with QIIME2
- [#239](https://github.com/nf-core/ampliseq/pull/239) - Support of RDP database for DADA2 classification
- [#237](https://github.com/nf-core/ampliseq/pull/237) - Support of UNITE database for DADA2 classification
- [#229](https://github.com/nf-core/ampliseq/pull/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](https://github.com/nf-core/ampliseq/pull/229) - `--sample_inference`, `--concatenate_reads`, `--illumina_pe_its`; please check the documentation for their function
- [#275](https://github.com/nf-core/ampliseq/pull/275) - Read count summary
- [#274](https://github.com/nf-core/ampliseq/pull/274) - `--skip_qiime` to prevent any steps that are executed with QIIME2
- [#272](https://github.com/nf-core/ampliseq/pull/272) - `--cut_its` to cut ASV sequence to ITS region before performing taxonomic classification with DADA2
- [#280](https://github.com/nf-core/ampliseq/pull/280) - Added support for IonTorrent data
- [#283](https://github.com/nf-core/ampliseq/pull/283) - `--cut_dada_ref_taxonomy` allows extracting expected amplicons from DADA2 reference taxonomy database

### `Changed`

- [#254](https://github.com/nf-core/ampliseq/pull/254) - Updated CamelCase parameters to be lower_case_snake_case:
  - `multipleSequencingRuns` to `multiple_sequencing_runs`
  - `minLen` to `min_len`
  - `maxLen` to `max_len`
  - `maxEE` to `max_ee`
- [#277](https://github.com/nf-core/ampliseq/pull/277) - Requires nextflow version `>= 21.04.0`

### `Fixed`

- [#273](https://github.com/nf-core/ampliseq/pull/273) - Template update for nf-core/tools version 1.14

### `Dependencies`

- [#272](https://github.com/nf-core/ampliseq/pull/272) - New dependency ITSx v1.1.3
- [#229](https://github.com/nf-core/ampliseq/pull/229) - Updated from cutadapt v2.8 to v3.2
- [#229](https://github.com/nf-core/ampliseq/pull/229) - Updated DADA2 from v1.10 to v1.18.0, now not using QIIME2 for ASV generation any more
- [#229](https://github.com/nf-core/ampliseq/pull/229) - Updated QIIME2 to v2021.2

### `Removed`

- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--manifest` is superseeded by `--input` that can now also handle a sample sheet file input (required extension: `.tsv`)
- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--Q2imported` and `untilQ2import` are removed because pausing at that point is not neccessary
- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--split` is no longer supported, therefore all sample IDs have to be unique
- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--classifier_removeHash` and `--qiime_timezone` became unnecessary
- [#229](https://github.com/nf-core/ampliseq/pull/229) - `--onlyDenoising` is deprecated in favour of `--skip_taxonomy` (which does the exact same thing)
- `--taxon_reference` became unnecessary
- [#229](https://github.com/nf-core/ampliseq/pull/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" - 2021-02-04

### `Added`

- [#106](https://github.com/nf-core/ampliseq/issues/106) - Added support for PacBio data
- Added `--taxon_reference` to be able to support both 'silva' and 'unite'
- [#157](https://github.com/nf-core/ampliseq/issues/157) - Added possibility to run double cutadapt steps, `--double_primer`
- [#211](https://github.com/nf-core/ampliseq/issues/211) - Added quality filter option `--maxEE`

### `Fixed`

- [#182](https://github.com/nf-core/ampliseq/issues/182) - Fix input in case there are no underscores in sample IDs
- [#186](https://github.com/nf-core/ampliseq/issues/186) - Update github actions
- [#187](https://github.com/nf-core/ampliseq/issues/187) - Sample ids are in incorrect order in feature-table from PacBio data
- [#201](https://github.com/nf-core/ampliseq/pull/201) - Template update for nf-core/tools version 1.12.1
- [#147](https://github.com/nf-core/ampliseq/issues/147) - Split `make_classifier` in two different processes that can be allocated different resources
- [#183](https://github.com/nf-core/ampliseq/issues/183) - Don't fetch taxonomy/create classifier when run with `--skip_taxonomy`
- [#180](https://github.com/nf-core/ampliseq/issues/180) - MultiQC, cutadapt and fastQC now work with `--multipleSequencingRuns`

### `Dependencies`

- Updated from cutadapt v2.6 to v2.8

### `Deprecated`

## nf-core/ampliseq version 1.1.3 - 2020-11-02

### `Added`

- [#170](https://github.com/nf-core/ampliseq/issues/170) - Cite paper for initial release
- [#111](https://github.com/nf-core/ampliseq/issues/111) - Added parameter for user specified manifest file
- [#118](https://github.com/nf-core/ampliseq/issues/118) - Added social preview images
- [#135](https://github.com/nf-core/ampliseq/issues/135) - Added `--trunc_rmin` to make sure that auto trunc cutoff retaines a certain fraction of reads

### `Fixed`

- [#172](https://github.com/nf-core/ampliseq/pull/172) - Template update for nf-core/tools v1.11
- [#163](https://github.com/nf-core/ampliseq/pull/163) - Template update for nf-core/tools v1.10.2
- [#136](https://github.com/nf-core/ampliseq/issues/136) - Pipeline fails with remote working directory
- [#152](https://github.com/nf-core/ampliseq/issues/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 - 2019-12-19

- No further changes, except a bugfix for the [timezone](https://github.com/nf-core/ampliseq/issues/114) issue found by @marchoeppner
- Specification of `--qiime_timezone` might be required to run the analysis appropriately

## nf-core/ampliseq version 1.1.1 - 2019-12-09

### Pipeline Updates

- 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

### Bugfixes

- [#78](https://github.com/nf-core/ampliseq/issues/78) - All sequenced classifed to the same species

## nf-core/ampliseq version 1.1.0 "Silver Lime Bee" - 2019-07-15

### Pipeline updates

- [#40](https://github.com/nf-core/ampliseq/issues/40) - Added support for data originating from multiple sequencing runs
- [#53](https://github.com/nf-core/ampliseq/issues/53) - DADA2 report is always exported
- [#49](https://github.com/nf-core/ampliseq/issues/49) - Allowed more filtering options
- [#5](https://github.com/nf-core/ampliseq/issues/5) - Introduced check for existence of input files
- Extended parameter sanity check, including [#15](https://github.com/nf-core/ampliseq/issues/15)
- [#61](https://github.com/nf-core/ampliseq/issues/61) - Improved documentation
- [#62](https://github.com/nf-core/ampliseq/pull/62) - Utilize nf-core/configs centrally for this pipeline
- [#63](https://github.com/nf-core/ampliseq/issues/63) - QIIME imports files by using a manifest, giving more freedom with input file names
- [#84](https://github.com/nf-core/ampliseq/issues/84) - Add proper nf-core logo

### Bug fixes

- [#57](https://github.com/nf-core/ampliseq/issues/57) - Indicate exact regex for sequencing file names
- [#60](https://github.com/nf-core/ampliseq/issues/60) - publish demux.qza when --untilQ2import

## nf-core/ampliseq version 1.0.0 "Olive Steel Panda" - 2018-11-23

Initial release of nf-core/ampliseq, created with the [nf-core](http://nf-co.re/) template.
