metaflow 1.0.2

Added

• #79 - Support for pre-computed assemblies: Adds --assembly_input parameter to allow execution of metaflow pipeline using pre-computed assemblies, when provided together with the standard reads input (--input), the pipeline skips read preprocessing and assembly steps and starts directly from the binning stage.
• Assembly input specification
  • Assembly input must be supplied as a CSV file containing the columns: sample_id, run_id, group, assembler, fasta.
  • sample_id, run_id, and group follow the same schema as the primary reads input.
  • assembler specifies the assembly tool used (MEGAHIT or SPAdes).
  • fasta defines the path to the assembly FASTA file. Both compressed and uncompressed FASTA files are supported; compressed files are automatically decompressed within the pipeline.
• Consistency with reads input
  • Reads must still be supplied via --input, and only the CSV format (--input_format csv) is supported when using --assembly_input.
  • For single-sample assemblies, sample_id and group must match the corresponding entries in the reads CSV.
  • The reads provided should correspond to those used to generate the assemblies (e.g., adapter-trimmed or run-merged).
  • When pre-computed assemblies are supplied, all read preprocessing steps are skipped.

Changed

• Updated rgi to v6.0.5.
• Use aria2 to download rgi database.

Fixed

• #80 - Adjusts the logic for resolving the CheckM2 database when the user does not explicitly provide a path via --checkm2_db.
• #80 - Fixes an issue related to loading the CheckM database and downloading CheckM2 database from Zenodo.

Dependencies

Tool	Previous	New
rgi	6.0.3	6.0.5

Details

Full changelog: 1.0.1...1.0.2

metaflow 1.0.1

Added

• #75 Introduced --skip_yacht to bypass execution of the YACHT module.
• #76 Added --skip_preprocess to skip the PREPROCESS subworkflow. When enabled, the pipeline forwards input_ch directly as the cleaned_reads_source for the READ_BASED and ASSEMBLY_BASED subworkflows.
• #77 Added support for running sourmash & YACHT in single-sketch mode via --enable_singlesketch.
  Note: Single-sketch mode is slower because sourmash sketches samples one-by-one using a single thread.

Changed

• Updated SemiBin2 to v2.2.1.

Fixed

• Fixed compatibility issues where databases fetched via HOSTILE_FETCH could not be used in the HOSTILE_CLEAN step.
• Resolved severe slowdown during “Predicting CDS sequences with Pyrodigal” in Binette’s bin-refinement workflow (see upstream issue #92).
• Applied a temporary compatibility fix for Bakta when used with DIAMOND v2.1.19 (see upstream issue #418).

Dependencies

Tool	Previous	New
SemiBin2	2.1.0	2.2.1

Deprecated

• Removed legacy resource options due to compatibility issues.

Details

Full changelog: 1.0.0...1.0.1

metaflow 1.0.0

This is the first official release of metaflow 🍻. In this release, we introduce an assembly-based workflow as the primary pipeline. The read-based workflow used in the previous beta version has been retained as an optional feature and can be re-enabled in this official release using the --enable_readbase option.

Changed

• Update logo and workflow diagram images by @tnmquann in #37
• Add hostile by @tnmquann in #36
• Add params for adjusting computing resource allocation by @singuyenmai in #43
• RGI_BWT module and refactoring code by @tnmquann in #44
• Add contig analysis workflow by @tnmquann in #47
• Implemented Prokka and Pyrodigal module for contigs annotation by @tnmquann in #49
• Add bin refinement subworkflow by @tnmquann in #55
• Add subworkflow for bin quality evaluation by @tnmquann in #61
• Add subworkflow for domain classification by @tnmquann in #67
• Add subworkflow for bin classification annotation by @tnmquann in #68

New Contributors

• @singuyenmai made her first contribution in #43

Full Changelog: beta...1.0.0

metaflow 0.0.1

We are pleased to announce the beta release of metaflow, featuring support for the taxonomic classification step. This version focuses on enabling accurate and efficient taxonomic profiling from metagenomic reads.
Please note that this version is still under active development and may undergo further updates before the final release.
Feedback and issue reports are welcome.

metaflow 0.0.1b2

• Pipeline Refactoring
  The pipeline has been restructured to follow a clear module/subworkflow model, improving maintainability and extensibility (by @tnmquann, @singuyenmai ).

• New option: --enable_rgi_bwt (by @tnmquann)
  #10 : Added a configurable option --enable_rgi_bwt (default: false). When enabled, this option aligns metagenomic reads to the CARD and wildCARD reference databases and generates comprehensive antibiotic resistance gene detection reports.

  • By default, the option automatically downloads and indexes the CARD database and stores it in the output folder.
  • Users can alternatively provide a pre-indexed CARD database using the --rgi_preparecarddb_dir parameter.