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Ampliseq Version 2.0.0 "Blue Copper Kangaroo"
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@d4straub d4straub released this 29 Jun 10:52
· 1687 commits to master since this release
2.0.0
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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 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
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