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nf-core/ampliseq: Changelog

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

nf-core/ampliseq version 2.2.0dev

Added

  • # - Make --skip_dada_addspecies compatible with --cut_its
  • #352 - --skip_dada_addspecies allows to skip species level classification to reduce memory requirements, incompatible with --sbdiexport and --cut_its that expect species annotation
  • #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.
  • #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

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

Fixed

  • #362- Template update for nf-core/tools version 2.2, now requires nextflow version >= 21.10.3

Dependencies

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.
  • 342 - Added PICRUSt2 to summary figure.

Fixed

  • #329 - Improve error message when no data files are found
  • #330 - Make --skip_fastqc usable again
  • #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 - 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/ 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)
  • #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

  • #299 - Updated MultiQC to v1.10
  • #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 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
  • #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 to multiple_sequencing_runs
    • minLen to min_len
    • maxLen to max_len
    • maxEE to max_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 and untilQ2import 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" - 2021-02-04

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 - 2020-11-02

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 - 2019-12-19

  • 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 - 2019-12-09

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 - All sequenced classifed to the same species

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

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.