Skip to content

CHANGELOG.md

Latest commit

 

History

History
120 lines (98 loc) · 8.07 KB

CHANGELOG.md

File metadata and controls

120 lines (98 loc) · 8.07 KB

Changelog

All notable changes to this project will be documented in this file.

This project tries to adhere to Semantic Versioning.
For version numbering, we use the following convention: MAJOR.MINOR.PATCH.
Each element increases numerically (e.g., 1.9.0 -> 1.10.0 -> 1.11.0).

[1.2.0] - 2026-XX-XX

  • Fixed a bug with demultiplexing using dual tags (sometimes files were named as unknown tag combinations)
  • Add automatic detection of "single-library" results in Step-2

[1.1.0] - 2026-01-22

  • Fixed handling of unknown barcode combinations (in dual asymmetric mode); thanks to Alice Retter for reporting
  • Refactored and optimized the tag-jump removal step
  • Fixed a bug with duplicated sequences in the tag-jump removal step; thanks to Valentin Étienne for reporting
  • Implemented a chunking option for splitting the dataset into smaller parts prior to clustering in Step-2 (pre-clustering, clustering, and denoising moved to a separate sub-workflow), using MMseqs2
  • Added possibility to disable reference-based and/or de novo chimera removal steps and tag-jump removal
  • New parameters added:
    • lima_remove_unknown (default, false; if true, unknown barcode combinations are removed from demultiplexed data)
    • chunking_n (number of chunks to split the dataset into prior to clustering)
    • chunking_id (minimum sequence identity used for splitting the dataset into chunks)
    • chimera_methods (specifies which chimera removal methods to use - "ref" for reference-based, "denovo" for de novo, or "ref,denovo" for both; could be also "none" or null to disable chimera removal)
    • tj (specifies whether to run tag-jump removal - "true" or "false")
  • Added DADA2 denoising (--preclustering dada2; also works with --clustering none)
  • Implemented automated documentation for analysis procedures (generates README_Step1_Methods.txt and README_Step2_Methods.txt in the pipeline_info directory)
  • Refactored parameter validation (using nf-schema plugin)
  • Refactored the runtime parameter summary and help message
  • Added test profiles (test, test1, test2)
  • Improved run summary for Step-1
  • Default parameters changed:
    • ITSx now checks only a single strand (option ITSx_complement set to F). This should be safe for most cases, as amplicons were re-oriented using primers during the pipeline run. However, we recommend checking the results carefully (e.g., columns ITSx_Extracted_Reads and ITSx_Yield_Percent in the run summary)
    • Prior to tag-jump removal, sequences are now dereplicated at 100% identity (option tj_id set to 1). It is possible to pre-cluster sequences at a lower similarity threshold (e.g., --tj_id 0.99) but this will take much longer. This change should also be safe for most cases, as amplicons undergo homopolymer-correction
  • Fixed a minor bug in extraction of sample IDs at the ref-based chimera rescue step; thanks to Valentin Étienne for reporting

[1.0.0] - 2025-03-24

  • Added support of asymmetric barcoding scheme for demultiplexing of PacBio data
  • Added support of BAM files (CCS) as input
  • Added support for SWARM d=1 pre-clustering
  • Changed the selection of representative sequences (sequence with the highest quality score is taken as the representative; using phredsort)
  • Refactored sequence quality estimation
  • Improved processing speed (using DuckDB and Parquet format)
  • Improved tag valiadion for demultiplexing
  • Improved compression speed for output files (runs in parallel using pigz)
  • Update of the database for reference-based chimera detection (using the EUKARYOME database)
  • New parameters added:
    • step (specifies which pipeline step to run - "Step1" or "Step2")
    • storagemode (Adjusts how files are directed to the results folder)
    • gzip_compression (Controls GZIP compression level in output files)
    • categorical lima_barcodetype replaces boolean lima_dualbarcode
    • lima_minendscore (For asymmetric and dual barcoding scheme)
    • lima_minrefspan (Controls barcode coverage)
    • lima_minscoringregions (Controls the number of reqired barcodes for demultiplexing using dual barcodes)
  • Added auxilarry output files:
    • [Step-1] All rRNA parts extracted by ITSx (pooled within sequencing run - useful for extracting these regions for representative sequences)
    • [Step-1] File with quality scores for full-length sequences (after QC and trimming)
    • [Step-2] File with joined sequence memebership (dereplication, pre-clustering, and clustering)
  • Primer trimming prior ITSx is now default (sequence quality is also estimated on trimmed sequence)
  • Fixed VSEARCH clustering on denoised reads
  • Resolved an issue where no de novo chimeras were detected
  • Reconfigured parameter specification
  • Introduced a parameter schema and enhanced parameter validation
  • Container updates to included the latest versions of dependencies
  • New dependencies - specialized tools written in Go to speed up the processing:

[0.5.0] - 2023-08-08

  • New seqstats sub-workflow (only dereplication, primer validation, and basic run stats)
  • Add SWARM clustering (Mahé et al., 2022 DOI:10.1093/bioinformatics/btab493)
  • Add post-clustering curation with LULU (Frøslev et al., 2017 DOI:doi.org/10.1038)
  • Add barcode validation step
  • Add SSU and LSU region-based output sequences
  • Add support for UNOISE-only output (without clustering)
  • Add merge_replicates parameter (Step-2) for merging or keeping separate sample replicates
  • Update Step-1 run summary (add homopolymer stats)
  • Deprecate taxonomy annotation workflow at Step-1
  • Fixed different extensions in demultiplexed input
  • Experimental: UNITE-style dereplication (allows query sequences to vary in length at 100% similarity)
  • Experimental: support of alternative alignment penalty scores (ITS-specific feature)

[0.4.0] - 2023-05-08

[0.3.0] - 2023-03-02

  • Add support for pre-demultiplexed data as input
  • Add option for semi-full-length ITS (especially useful when forward primer is located at the very end of SSU and the HMM site can not be recognized by ITSx)
  • Add removal of long homopolymer artefacts at QC stage
  • Correct handling of a case with no valid sequences at primer checking step (thank to Taavi Riit for reporting the bug)
  • Bug fixed in assemble_its (thanks to Kadri Põldmaa for discovering the error)
  • Addition of ITSx detailed results (with information on the HMM profile used for ITS extraction)
  • Fixed sample names for the rescued chimeric sequences
  • Minor fixes related with the Singularity container, output directory, help message, and single-end QC

[0.2.0] - 2022-09-30

  • Add Ilumina-based workflow (see --seqplatform flag)
  • Publish Singularity image to Singularity library
  • Minor bugfixes in primer_check (multiprimer artefacts), pool_seqs (sequence headers), and prep_asvtab (aggregation of non-unique joined Illumina sequences) processes
  • New logo design (thanks to Olesya Dulya)

[0.0.1] - 2022-07-07

  • Initial release