nf-core/ampliseq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

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

`Deprecated`

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
Export absolute abundance files into 'results/abundance-table/filtered/' for optional external secondary analysis

Bugfixes

#78 - All sequenced classifed 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

#57 - Indicate exact regex for sequencing file names
#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 template.