upd NextITS to 1.1.0 - #12
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Pull request overview
This pull request updates NextITS from version 1.0.0 to 1.1.0. The update includes significant enhancements to the bioinformatics pipeline for processing eukaryotic ITS amplicons with PacBio sequencing data. Key changes include adding support for processing dereplicated data without clustering, refactoring the ITSx processing workflow into a dedicated subworkflow, updating container definitions with newer software versions, and adding new configuration parameters.
Changes:
- Added new workflow for handling dereplicated sequences without clustering/denoising
- Refactored ITSx processing into a dedicated subworkflow with chunking support
- Updated container dependencies (Rust 1.92.0, R 4.5.2, DuckDB 1.4.3, and various bioinformatics tools)
- Added new parameters:
ITSx_chunk_size,chimera_methods,tj - Fixed handling of ITSx extraction results compression
Reviewed changes
Copilot reviewed 17 out of 47 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| STEP2.nf | Modified merge_buckets process to handle FASTA files for pre-clustering; added summarize_dereplicated_data process for non-clustered workflow |
| STEP1.nf | Fixed ITSx extraction results file compression (.gz extension) |
| itsx_subworkflow.nf | New subworkflow for distributed ITSx processing with chunking support |
| clustering_subworkflow.nf | Added preclustaf_ch channel to track pre-clustered FASTA files |
| nextflow_schema.json | Added ITSx_chunk_size parameter |
| Container files | Updated software versions (Rust, R, DuckDB, vsearch, swarm, etc.) |
| summarize_dereplicated_data.R | New R script for summarizing dereplicated data without clustering |
| CHANGELOG.md | Updated with version 1.1.0 release date and changes |
| CITATION.cff | Updated version to 1.1.0 |
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@METS0JA , Which NextITS code is actually used? |
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