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 #31
• Add support for error-free reads in art_illumina with --errfree by @teojcryan in #33

Changes

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

Fixes

• Fix duplicated fasta paths when samples use same genomes by @farchaab in #24
• Fix taxonomic abundances by @farchaab in #29

New Contributors

• @teojcryan made their first contribution in #33

Full Changelog: v0.9.0...v0.10.0

Release 0.9.0

Summary

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

Additions

• f9d8d50 c13af00 b01a258 Added containers in rules
• 86ec471 Added CITATION.cff

Changes

• 8ce623e Generate both sequence and taxonomic abundances by default
• aa00806 Moved conda envs to workflow/envs/conda
• d3159ab Removed utils env
• 88c8542 Added curl env
• 77241fc Added pigz env
• 59a4745 Froze versions in conda envs
• 4f79f28 Changed snakemake_run function to support --software-deployment-method from snakemake (apptainer or conda)
• dba5c92 Bumped minimal python version to 3.11 (snakemake version 8 and up, requires python >=3.11)
• 15e9f39 Added apptainer install in Dockerfile
• 8ce623e Generate both taxonomic and sequence abundance CAMI profile

Fixes

• 2a7a5d8 Changed default seed (Fixes truncated bam file in mess test --bam)

Github workflows

• afe8d09 82e3ac8 Fixed github workflow paths

Full Changelog: v0.8.3...v0.9.0

v0.8.3

Summary

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

Additions

• 26ff9a3 130a060 Added choice of taxonomic or sequence abundance in ground truth taxonomic profile

Changes

• f6b73b1 Added all assembly_finder dependencies in the yaml
• 5ecb186 Download reference genomes by default
• d642f51 Docs update
• fdd8611 d418233 Moved directories

Fixes

• 19e0bad Fixed taxonomic abundance calculation

Github workflows

• dfced09 6d06747 ff039d2 Added docker-publish

Full Changelog: v0.8.2...v0.8.3

mess v0.8.2

Summary

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

Changes

4bcd2ff Update assembly_finder rule to work with its latest version
3a7e8cf 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

d6dd6ac Renamed docs workflow
ed021e3 Restrict unit tests to python 3.12 and macOS to 13

Full Changelog: v0.8.0...v0.8.2

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 #17

New Contributors

• @farchaab made their first contribution in #16

Full Changelog: v0.2.2...v0.8.0

v0.2.2

Submodule merge

• Merged assembly_finder in the main repo 7248898
• Updated readme 30b44dd

v0.2.1

Small fixes

• Added option to generate a different log-normal distribution for each replicate 88c6550
• Added option to generate the same log-normal distribution for each replicate 43ca2f6
• Generate taxonomy and krona plot for each read pairing 8dc1b05
• Fixed conda prefix path 04f993b
• Updated messenv.yaml and removed requirements in setup.py 12a7f02 5874187

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

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