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Recent Releases of mess

mess - MeSS v0.12.0

MeSS v0.12.0 - 04-09-2025

🚀 Features

  • Addition of short reads amplicon simulation from local @farchaab (#49) and downloaded fasta @farchaab (#48)

🔧 Maintenance

  • Update apptainer mounts and add @farchaab art-args (#51)
  • Compress reads in simulators rule @farchaab (#50)
  • Tweak long reads length and error rates @farchaab (#59)

🐛 Bug Fixes

  • Fix download when no reference genomes @farchaab (#60)
  • Fix --custom-tax argument to prevent TypeError @teojcryan (#58)

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.11.0...v0.12.0

- Python
Published by github-actions[bot] 6 months ago

mess - v0.11.0

MeSS v0.11.0 - 06-05-2025

✨ Features

  • Add support for custom taxonomy https://github.com/metagenlab/MeSS/pull/46

🔧 Changes

  • Add paper citation https://github.com/metagenlab/MeSS/pull/38
  • Update conda envs https://github.com/metagenlab/MeSS/pull/43
  • Remove tax_id requirement in input table https://github.com/metagenlab/MeSS/pull/46
  • fasta column now requires fasta file base name https://github.com/metagenlab/MeSS/pull/46
  • Add read counts, coverage depth and breadth in ground truth tax profiles https://github.com/metagenlab/MeSS/pull/46
  • Add taxonomy type (custom or NCBI) with its date in @TaxonomyID for CAMI profiles https://github.com/metagenlab/MeSS/pull/46

:bug: Bug fixes

  • Fix unit tests https://github.com/metagenlab/MeSS/pull/39
  • Fix apptainer fasta paths mount https://github.com/metagenlab/MeSS/pull/46

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.10.0...v0.11.0

- Python
Published by farchaab 10 months ago

mess - v0.10.0

MeSS v0.10.0 - 20-11-2024

Set apptainer as default software deployment method, fixed taxonomic abundances, added circular genome simulations and bug fixes.

Features

  • Add support for circular genomes by @farchaab in https://github.com/metagenlab/MeSS/pull/31
  • Add support for error-free reads in art_illumina with --errfree by @teojcryan in https://github.com/metagenlab/MeSS/pull/33

Changes

  • Add ps in container and fix wildcards constraints by @farchaab in https://github.com/metagenlab/MeSS/pull/23
  • Change hmp-template download from taxids to accessios by @farchaab in https://github.com/metagenlab/MeSS/pull/30
  • Change default sdm to apptainer by @farchaab in https://github.com/metagenlab/MeSS/pull/34
  • Optimize read processing and functions by @farchaab in https://github.com/metagenlab/MeSS/pull/35
  • Optimize unit tests by @farchaab in https://github.com/metagenlab/MeSS/pull/36
  • Add SLURM profile in mess/profiles/slurm by @farchaab in https://github.com/metagenlab/MeSS/pull/37

Fixes

  • Fix duplicated fasta paths when samples use same genomes by @farchaab in https://github.com/metagenlab/MeSS/pull/24
  • Fix taxonomic abundances by @farchaab in https://github.com/metagenlab/MeSS/pull/29

New Contributors

  • @teojcryan made their first contribution in https://github.com/metagenlab/MeSS/pull/33

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.9.0...v0.10.0

- Python
Published by farchaab over 1 year ago

mess - Release 0.9.0

Summary

Release to add containers, freeze conda env versions, and other small fixes

Additions

  • f9d8d507effe6482c544e1a9cc5e24b118aae828 c13af00ef7a16a9e0d6a632fc972f0911231cdcc b01a258832f9c6bbe53679cb02cd93051c5c34c8 Added containers in rules
  • 86ec47104025b808b2e04c3d2e4d700cd6ceda81 Added CITATION.cff

Changes

  • 8ce623e Generate both sequence and taxonomic abundances by default
  • aa008066706b85a919f0e900d2d5b563389c5e9b Moved conda envs to workflow/envs/conda
  • d3159ab68c14a986c0b19265f744bc30e3c9e5aa Removed utils env
  • 88c8542be1a166763fd5013ad93e700db0f4b4ea Added curl env
  • 77241fc1c9c2ae3c5800761bf0aa627c07fd708d Added pigz env
    • 59a47452c72e8d0a26b72b01c71c890e0561877b Froze versions in conda envs
  • 4f79f28cb5b32f8d80afe9219c90ce65c3676e53 Changed snakemake_run function to support --software-deployment-method from snakemake (apptainer or conda)
  • dba5c92675d195b5f3d3e586e12bcc8c05cb7f4c Bumped minimal python version to 3.11 (snakemake version 8 and up, requires python >=3.11)
  • 15e9f39a040d8f85b00d741092ddac3c309a1993 Added apptainer install in Dockerfile
  • 8ce623e4da7d6f73b4f4d9cfd8b37612100c1d37 Generate both taxonomic and sequence abundance CAMI profile ## Fixes
  • 2a7a5d89ab8505017c414d48a4083f296c7351b2 Changed default seed (Fixes truncated bam file in mess test --bam)

Github workflows

  • afe8d09 82e3ac8 Fixed github workflow paths

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.8.3...v0.9.0

- Python
Published by farchaab over 1 year ago

mess - v0.8.3

Summary

Small release to add choice of abundance in taxonomic profile, fix taxonomic abundance and update docs

Additions

  • 26ff9a3f3d74d586f59a6f3a04d03f9008d25ab3 130a060445efb66c062df4e05fadb86d7a44b5ea Added choice of taxonomic or sequence abundance in ground truth taxonomic profile

Changes

  • f6b73b1577be05377d04bb553a410175fc9509da Added all assembly_finder dependencies in the yaml
  • 5ecb1865830902e4507726d5080874f76926412f Download reference genomes by default
  • d642f512090569b2db5d14eb3225673e6b732483 Docs update
  • fdd86119e5679fb59121a76f7267de3a77b07a9e d4182338f75dcf00e008fc090c0fd149d7368a76 Moved directories ## Fixes
  • 19e0badcfd5e39562b43fe766ce449a62d4c3163 Fixed taxonomic abundance calculation

Github workflows

  • dfced096fd55a8bd50d9834faea5cab224281155 6d0674789bc31d34845c4ef6518193c0b29541dd ff039d23bc3ff3189c72035b2575595970fcf5e4 Added docker-publish

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.8.2...v0.8.3

- Python
Published by farchaab almost 2 years ago

mess - mess v0.8.2

Summary

Small release to work with assembly_finder version 0.7.1, fix hmp templates and temp files cleanup

Changes

4bcd2ff78f8a00405c455df53dfe8162c9c4d736 Update assembly_finder rule to work with its latest version 3a7e8cfd21a0e695f64008e8c4c4ad1911aa7927 Merged tar, sed, curl and pigz in a single env e730b14 Changed cov.tsv path c06ebd7 Changed split directory path

Fixes

38cdff8 Fixed hmp templates inputs d83e6d6 Fixed --limit arg 430c8ef 357e786 8412730 Fixed temp dir and files cleanup

Github workflows

d6dd6ac0fec55de0ee00bcfa541fc5a51b349e74 Renamed docs workflow ed021e3b3930fe7fb77fec20f0960396477671da Restrict unit tests to python 3.12 and macOS to 13

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.8.0...v0.8.2

- Python
Published by farchaab almost 2 years ago

mess - Release v0.8.0

Summary

Big release with bug fixes and new features: * Refactored code with snaketool * Simplified input sample sheet (no more camelCase) * Added commands for main steps of the workflow (genome download, read simulation...) * Multiple samples with different communities can be simulated in a single run * Updated long reads to support ONT r10.4.1 and PacBio hifi read generation * Read simulation with local genomes * Optionally generate bam and taxonomic profiles in bioboxes format * Nice rich formatted cli with rich-click * Built documentation on metagenlab.github.io/MeSS/ * Added unit tests in github actions

Details

  • Check detailed changes by @farchaab in https://github.com/metagenlab/MeSS/pull/17

New Contributors

  • @farchaab made their first contribution in https://github.com/metagenlab/MeSS/pull/16

Full Changelog: https://github.com/metagenlab/MeSS/compare/v0.2.2...v0.8.0

- Python
Published by farchaab almost 2 years ago

mess - v0.2.2

Submodule merge

  • Merged assembly_finder in the main repo https://github.com/metagenlab/MeSS/commit/72488985ee543f9547f877fb30116892ca3d89d0
  • Updated readme https://github.com/metagenlab/MeSS/commit/30b44dd4c53b01fa0ff5b122929376c76495c351

- Python
Published by idfarbanecha over 4 years ago

mess - v0.2.1

Small fixes

  • Added option to generate a different log-normal distribution for each replicate https://github.com/metagenlab/MeSS/commit/88c6550b0916af29c3c09460d2269ca6eb5b2dea
  • Added option to generate the same log-normal distribution for each replicate https://github.com/metagenlab/MeSS/commit/43ca2f681ce062a9349e7d20257bcb29ee1f8505
  • Generate taxonomy and krona plot for each read pairing https://github.com/metagenlab/MeSS/commit/8dc1b05585a88c2a39b1b7713ff704a6ce570e25
  • Fixed conda prefix path https://github.com/metagenlab/MeSS/commit/04f993b10aa9f5506b796f3ad3b808595312d77e
  • Updated messenv.yaml and removed requirements in setup.py https://github.com/metagenlab/MeSS/commit/12a7f02f1cccd25f98858aa5ab24177c603a91bc https://github.com/metagenlab/MeSS/commit/58741874599ab5cce0801d90879980a56a2ab447

- Python
Published by idfarbanecha over 4 years ago

mess - v0.2.0

Added several features

Features

  • Added assembly names and Genbank UID as possible inputs
  • Added the possibility to generate read abundances from a log-normal distribution
  • Added the possibility to generate read abundances from an even distribution between superkingdoms
  • Added parameter to generate BAM files
  • The user can add a path in the config file (assemblies_dir parameter) that points to already downloaded assemblies

- Python
Published by idfarbanecha over 4 years ago

mess - First release

Working pipeline to generate in-silico mock communities.

Features:

  • #1 Genome coverage as input
  • #2 Relative abundance as input
  • #3 Conda package
  • #4 Long reads support with pbsim2

- Python
Published by idfarbanecha almost 5 years ago