feat: added wrapper for MOFA2 #4883
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📝 WalkthroughWalkthroughAdds a new MOFA2 wrapper: conda environment definitions (YAML and pinned), package metadata, an R wrapper that trains MOFA2 from Parquet, a Snakemake test rule, .gitattributes, and an accompanying test addition. Changes
Sequence Diagram(s)sequenceDiagram
participant Snakemake as Snakemake Rule
participant Wrapper as wrapper.R
participant MOFA2 as MOFA2 Library
participant Input as Parquet Input
participant Output as HDF5 Output
Snakemake->>Wrapper: Execute with params (scale_groups, scale_views), input/output paths
Wrapper->>Input: Read parquet (sample, feature, view, group, value)
Wrapper->>MOFA2: Load libs and create MOFA object
Wrapper->>MOFA2: Apply scaling options and prepare model
Wrapper->>MOFA2: Train model (run_mofa)
MOFA2->>Output: Write trained model to HDF5
Output-->>Snakemake: HDF5 produced
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~22 minutes 🚥 Pre-merge checks | ✅ 2 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (2 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing touches
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Actionable comments posted: 2
🧹 Nitpick comments (4)
.gitattributes (1)
1-2: Minor inconsistency with subdirectory .gitattributesThe root
.gitattributesis missing the-diffflag that's present inbio/mofa2/.gitattributes. While not critical, it's worth checking whether both should consistently prevent diff generation forpixi.lockfiles.Root (Line 2):
pixi.lock merge=binary linguist-language=YAML linguist-generated=true
Bio/mofa2 (Line 2):pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diffbio/mofa2/meta.yaml (1)
15-15: Consider rephrasing the group parameter documentationThe current phrasing "Discouraged for beginners" might be overly cautionary. Consider rephrasing to be more informative while still indicating it's an advanced feature.
🔎 Suggested rephrasing
- `group` (optional, advanced): Discouraged for beginners. The aim of the multi-group framework is not to capture differential changes in mean levels between the groups (as for example when doing differential RNA expression). The goal is to compare the sources of variability that drive each group. + `group` (optional, advanced): The multi-group framework compares sources of variability across groups rather than capturing differential changes in mean levels (e.g., differential RNA expression). Consider omitting this column unless you specifically need to model multiple distinct biological groups.bio/mofa2/wrapper.R (2)
1-1: Consider using the standard portable shebang.The current shebang
#!/bin/Rassumes R is installed at/bin/R, which may not be true on all systems. The more portable form is#!/usr/bin/env Rscript.🔎 Proposed fix
-#!/bin/R +#!/usr/bin/env Rscript
35-51: Consider simplifying parameter handling withas.logical().The current implementation uses separate if statements to convert string parameters to boolean values. This works correctly but is verbose. R's
as.logical()function can convert "TRUE"/"FALSE" strings directly to boolean values.🔎 Proposed refactor
-if ("scale_groups" %in% names(snakemake@params)) { - if (snakemake@params[["scale_groups"]] == "FALSE") { - data_opts$scale_groups <- FALSE - } - if (snakemake@params[["scale_groups"]] == "TRUE") { - data_opts$scale_groups <- TRUE - } -} +if ("scale_groups" %in% names(snakemake@params)) { + data_opts$scale_groups <- as.logical(snakemake@params[["scale_groups"]]) +} -if ("scale_views" %in% names(snakemake@params)) { - if (snakemake@params[["scale_views"]] == "FALSE") { - data_opts$scale_views <- FALSE - } - if (snakemake@params[["scale_views"]] == "TRUE") { - data_opts$scale_views <- TRUE - } -} +if ("scale_views" %in% names(snakemake@params)) { + data_opts$scale_views <- as.logical(snakemake@params[["scale_views"]]) +}
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bio/mofa2/test/data.parquetis excluded by!**/*.parquetbio/mofa2/test/log/data.logis excluded by!**/*.logbio/mofa2/test/log/microbiome.logis excluded by!**/*.logbio/mofa2/test/microbiome.parquetis excluded by!**/*.parquet
📒 Files selected for processing (10)
.gitattributes.gitignorebio/mofa2/.gitattributesbio/mofa2/.gitignorebio/mofa2/environment.linux-64.pin.txtbio/mofa2/environment.yamlbio/mofa2/meta.yamlbio/mofa2/test/Snakefilebio/mofa2/wrapper.Rtest_wrappers.py
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**/*.py
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Files:
test_wrappers.py
🧠 Learnings (10)
📓 Common learnings
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3499
File: bio/ngscheckmate/makesnvpattern/test/Snakefile:14-22
Timestamp: 2024-11-26T09:16:39.570Z
Learning: In the `snakemake-wrappers` repository, when writing test `Snakefile`s (e.g., `bio/ngscheckmate/makesnvpattern/test/Snakefile`), hardcoded input/output paths are acceptable because these are examples and the IO can be chosen freely.
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/test/Snakefile:2-6
Timestamp: 2024-11-26T08:31:00.099Z
Learning: In test files for Snakemake wrappers, such as `bio/mtnucratio/test/Snakefile`, hard-coded input and output paths are acceptable as examples and do not need to use wildcards to make paths flexible.
📚 Learning: 2024-11-26T08:31:00.099Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/test/Snakefile:2-6
Timestamp: 2024-11-26T08:31:00.099Z
Learning: In test files for Snakemake wrappers, such as `bio/mtnucratio/test/Snakefile`, hard-coded input and output paths are acceptable as examples and do not need to use wildcards to make paths flexible.
Applied to files:
bio/mofa2/test/Snakefiletest_wrappers.py
📚 Learning: 2024-11-26T09:16:39.570Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3499
File: bio/ngscheckmate/makesnvpattern/test/Snakefile:14-22
Timestamp: 2024-11-26T09:16:39.570Z
Learning: In the `snakemake-wrappers` repository, when writing test `Snakefile`s (e.g., `bio/ngscheckmate/makesnvpattern/test/Snakefile`), hardcoded input/output paths are acceptable because these are examples and the IO can be chosen freely.
Applied to files:
bio/mofa2/test/Snakefile
📚 Learning: 2025-02-11T12:24:22.592Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 3648
File: bio/nanosim/simulator/environment.yaml:6-6
Timestamp: 2025-02-11T12:24:22.592Z
Learning: In the nanosim bioconda recipe, dependencies are carefully managed with specific version pins (e.g., scikit-learn ~=0.23.2) to ensure compatibility with pre-trained models. These dependencies don't need to be explicitly added to environment.yaml files when the main package is listed as a dependency, as they are handled through the bioconda recipe system.
Applied to files:
bio/mofa2/environment.yamlbio/mofa2/environment.linux-64.pin.txt
📚 Learning: 2025-04-17T09:24:51.738Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 0
File: :0-0
Timestamp: 2025-04-17T09:24:51.738Z
Learning: In snakemake-wrappers repository, environment.yaml files should follow these conventions:
1. Use whitespace before the equal sign in version specifications (e.g., "datavzrd =2.53.1")
2. Only specify the exact version for the main software package
3. Don't add version constraints for dependencies unless absolutely necessary
4. See full guidelines at: https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html#environment-yaml-file
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2025-04-17T09:24:51.738Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 0
File: :0-0
Timestamp: 2025-04-17T09:24:51.738Z
Learning: In snakemake-wrappers repository, environment.yaml files should follow these conventions:
1. Use whitespace before the equal sign in version specifications (e.g., "datavzrd =2.53.1")
2. Only specify the exact version for the main software package
3. Don't add version constraints for dependencies unless absolutely necessary
4. See guidelines at: https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html#environment-yaml-file
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2025-06-02T07:56:35.854Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 4159
File: bio/pyfaidx/environment.yaml:6-6
Timestamp: 2025-06-02T07:56:35.854Z
Learning: In the Snakemake-wrapper repository, conda dependency version pinning in environment.yaml files uses spaces around the equals sign (e.g., `- pyfaidx =0.8.1.4`) as the established coding standard, even though conda itself doesn't require the spaces.
Applied to files:
bio/mofa2/environment.yamlbio/mofa2/environment.linux-64.pin.txt
📚 Learning: 2024-11-21T10:23:03.427Z
Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/wrapper.py:5-12
Timestamp: 2024-11-21T10:23:03.427Z
Learning: In the Snakemake wrappers project, avoid suggesting extensive error handling or temporary file management in simple wrapper scripts when it may be unnecessary, to prevent overcomplicating the code.
Applied to files:
test_wrappers.pybio/mofa2/wrapper.R
📚 Learning: 2024-11-26T08:30:23.818Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/wrapper.py:27-28
Timestamp: 2024-11-26T08:30:23.818Z
Learning: In Snakemake wrappers (e.g., `wrapper.py` files), it's unnecessary to verify the availability of tools like `mtnucratio` within the code, because Snakemake with Conda ensures that the required tools are installed and available.
Applied to files:
test_wrappers.py
📚 Learning: 2024-11-26T10:49:54.765Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3501
File: meta/bio/varscan2_snpeff/test/Snakefile:58-71
Timestamp: 2024-11-26T10:49:54.765Z
Learning: In test Snakefiles within the snakemake-wrappers repository, it is acceptable to use simplified paths and logging configurations that may differ from real-life pipelines.
Applied to files:
test_wrappers.py
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: Summary
🔇 Additional comments (13)
bio/mofa2/.gitignore (1)
1-3: LGTM!The pixi environment ignore pattern is standard and appropriate. Tracking only
.pixi/config.tomlwhile ignoring the rest of the directory follows best practices.bio/mofa2/.gitattributes (1)
1-2: LGTM!Marking
pixi.lockas binary prevents merge conflicts while maintaining syntax highlighting. This is standard practice for lock files.test_wrappers.py (2)
271-280: LGTM - Command formatting improvementThe multi-line format improves readability of the command arguments.
7177-7178: LGTM - MOFA2 test follows repository patternsThe test follows the established pattern for wrapper tests in this repository. The minimal test approach (ensuring the wrapper executes without errors) is appropriate per repository conventions.
bio/mofa2/environment.linux-64.pin.txt (1)
1-267: LGTM - Standard explicit environment specificationThis explicit pin file follows conda best practices for reproducible environments. The
@EXPLICITformat with URL hashes ensures that exact package versions can be reconstructed. While lengthy, this is the expected format for fully pinned environments.bio/mofa2/meta.yaml (1)
1-26: Well-documented wrapper metadataThe metadata file provides clear documentation of the wrapper's purpose, input/output formats, and usage notes. The structured format with explicit column descriptions and parameter guidance will help users understand how to use the wrapper correctly.
bio/mofa2/environment.yaml (1)
6-10: The package versions specified are valid and currently available. Python 3.14.2 was released on December 5, 2025, MOFA2 v1.16.0 is available in Bioconda, and mofapy2 v0.7.2 is the latest release with no known security vulnerabilities. No action required.bio/mofa2/test/Snakefile (1)
1-12: LGTM!The rule structure is clean and follows Snakemake conventions. The wildcard pattern provides flexibility, and the inline parameter comments clearly explain when scaling should be enabled.
bio/mofa2/wrapper.R (5)
3-9: LGTM!The library loading and conda environment setup correctly handle MOFA2's Python dependencies through reticulate.
11-16: LGTM!The logging setup correctly redirects both standard output and messages to the Snakemake log file when provided.
18-24: LGTM!The input loading correctly casts the path to character (defensive programming) and the comment clearly documents the expected Parquet schema.
26-30: LGTM!The MOFA object creation and default options retrieval follow the standard MOFA2 workflow.
55-60: LGTM!The
prepare_mofacall correctly passes all configured options to finalize the MOFA object before training.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 3
🤖 Fix all issues with AI agents
In @bio/mofa2/wrapper.R:
- Around line 43-44: The comment in wrapper.R referencing training params
(maxiter, convergence_mode, gpu_mode, verbose) is stale; either remove that line
or implement those parameters by adding them to the relevant function signature
(e.g., the mofa2 training wrapper function in wrapper.R), pass them through to
the internal train routine (ensuring names match: maxiter, convergence_mode,
gpu_mode, verbose), validate types/values, and update any calls/tests; if you
choose removal, simply delete the comment to avoid confusion.
- Around line 39-41: The code mistakenly assigns
snakemake@params[["scale_views"]] to data_opts$scale_groups; change the
assignment so snakemake@params[["scale_views"]] is stored in
data_opts$scale_views instead, i.e., replace the reference to
data_opts$scale_groups with data_opts$scale_views in the block that checks
"scale_views" in names(snakemake@params) to restore the intended scale_views
behavior.
- Line 52: The output path currently builds outfile using file.path(getwd(),
snakemake@output[[1]]); remove the unnecessary getwd()/file.path wrapping and
set outfile to snakemake@output[[1]] directly so it matches other R wrappers
(e.g., saveRDS(..., snakemake@output[[1]])) and lets Snakemake handle path
resolution.
🧹 Nitpick comments (1)
bio/mofa2/wrapper.R (1)
1-1: Consider using a more standard shebang.The shebang
#!/bin/Ris non-standard. Consider using#!/usr/bin/env Rscriptfor better portability across systems, though in a Conda environment this may be less critical.♻️ Proposed fix
-#!/bin/R +#!/usr/bin/env Rscript
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📒 Files selected for processing (2)
bio/mofa2/test/Snakefilebio/mofa2/wrapper.R
🚧 Files skipped from review as they are similar to previous changes (1)
- bio/mofa2/test/Snakefile
🧰 Additional context used
🧠 Learnings (2)
📓 Common learnings
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/wrapper.py:27-28
Timestamp: 2024-11-26T08:30:23.818Z
Learning: In Snakemake wrappers (e.g., `wrapper.py` files), it's unnecessary to verify the availability of tools like `mtnucratio` within the code, because Snakemake with Conda ensures that the required tools are installed and available.
📚 Learning: 2024-11-21T10:23:03.427Z
Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3478
File: bio/varlociraptor/estimate-alignment-properties/wrapper.py:5-12
Timestamp: 2024-11-21T10:23:03.427Z
Learning: In the Snakemake wrappers project, avoid suggesting extensive error handling or temporary file management in simple wrapper scripts when it may be unnecessary, to prevent overcomplicating the code.
Applied to files:
bio/mofa2/wrapper.R
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: Summary
🔇 Additional comments (1)
bio/mofa2/wrapper.R (1)
7-9: Good implementation of MOFA2 workflow structure.The wrapper correctly:
- Connects to the Conda environment for MOFA2's Python backend via reticulate (lines 7-9)
- Implements standard log redirection for Snakemake (lines 11-16)
- Follows the proper MOFA2 workflow: create → configure → prepare → train (lines 26-30, 45-50, 54-58)
Please ensure the critical bug on line 40 is fixed before merging.
Also applies to: 11-16, 26-30, 45-50, 54-58
|
Thank you for your feedback. All issues should be fixed now. In manual local testing, the wrapper worked as intended. |
|
Is the |
From what I understand, yes. The training of the model is done in Python and the R-tool See the official installation guide: https://biofam.github.io/MOFA2/installation.html And the tutorial (section 6): https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/getting_started_R.html I thought it was better to use the conda environment provided by Snakemake and download |
|
But if |
Well, as I mentioned, they say in their documentation that |
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Actionable comments posted: 0
🧹 Nitpick comments (1)
bio/mofa2/environment.yaml (1)
5-8: Consider removing version pins from dependencies.Per the snakemake-wrappers guidelines, only the main software package should have an exact version pin, and version constraints for dependencies should be avoided unless absolutely necessary.
bioconductor-mofa2 =1.16.0— main package, version pin is appropriate ✓r-arrow =22.0.0andmofapy2 =0.7.2— these are dependencies; pinning may cause unnecessary solver conflicts during future updatesThe explicit inclusion of
mofapy2is justified (avoids basilisk creating a separate Python environment), but the version pin could be relaxed.Suggested change
dependencies: - bioconductor-mofa2 =1.16.0 - - r-arrow =22.0.0 - - mofapy2 =0.7.2 + - r-arrow + - mofapy2Based on learnings from this repository's environment.yaml conventions.
📜 Review details
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Review profile: CHILL
Plan: Pro
📒 Files selected for processing (2)
bio/mofa2/environment.linux-64.pin.txtbio/mofa2/environment.yaml
🧰 Additional context used
🧠 Learnings (8)
📓 Common learnings
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/wrapper.py:27-28
Timestamp: 2024-11-26T08:30:23.818Z
Learning: In Snakemake wrappers (e.g., `wrapper.py` files), it's unnecessary to verify the availability of tools like `mtnucratio` within the code, because Snakemake with Conda ensures that the required tools are installed and available.
📚 Learning: 2025-02-11T12:24:22.592Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 3648
File: bio/nanosim/simulator/environment.yaml:6-6
Timestamp: 2025-02-11T12:24:22.592Z
Learning: In the nanosim bioconda recipe, dependencies are carefully managed with specific version pins (e.g., scikit-learn ~=0.23.2) to ensure compatibility with pre-trained models. These dependencies don't need to be explicitly added to environment.yaml files when the main package is listed as a dependency, as they are handled through the bioconda recipe system.
Applied to files:
bio/mofa2/environment.yamlbio/mofa2/environment.linux-64.pin.txt
📚 Learning: 2025-04-17T09:24:51.738Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 0
File: :0-0
Timestamp: 2025-04-17T09:24:51.738Z
Learning: In snakemake-wrappers repository, environment.yaml files should follow these conventions:
1. Use whitespace before the equal sign in version specifications (e.g., "datavzrd =2.53.1")
2. Only specify the exact version for the main software package
3. Don't add version constraints for dependencies unless absolutely necessary
4. See full guidelines at: https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html#environment-yaml-file
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2025-04-17T09:24:51.738Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 0
File: :0-0
Timestamp: 2025-04-17T09:24:51.738Z
Learning: In snakemake-wrappers repository, environment.yaml files should follow these conventions:
1. Use whitespace before the equal sign in version specifications (e.g., "datavzrd =2.53.1")
2. Only specify the exact version for the main software package
3. Don't add version constraints for dependencies unless absolutely necessary
4. See guidelines at: https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html#environment-yaml-file
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2025-06-02T07:56:35.854Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 4159
File: bio/pyfaidx/environment.yaml:6-6
Timestamp: 2025-06-02T07:56:35.854Z
Learning: In the Snakemake-wrapper repository, conda dependency version pinning in environment.yaml files uses spaces around the equals sign (e.g., `- pyfaidx =0.8.1.4`) as the established coding standard, even though conda itself doesn't require the spaces.
Applied to files:
bio/mofa2/environment.yamlbio/mofa2/environment.linux-64.pin.txt
📚 Learning: 2024-10-31T10:01:29.976Z
Learnt from: johanneskoester
Repo: snakemake/snakemake-wrappers PR: 3374
File: utils/datavzrd/environment.yaml:7-9
Timestamp: 2024-10-31T10:01:29.976Z
Learning: In the `utils/datavzrd` wrapper, numpy, pandas, and polars are required dependencies because users can pass objects of these types via `params`, and since the wrapper evaluates them via YTE, these packages need to be present in the environment to support all potential params.
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2024-11-26T08:30:23.818Z
Learnt from: tdayris
Repo: snakemake/snakemake-wrappers PR: 3496
File: bio/mtnucratio/wrapper.py:27-28
Timestamp: 2024-11-26T08:30:23.818Z
Learning: In Snakemake wrappers (e.g., `wrapper.py` files), it's unnecessary to verify the availability of tools like `mtnucratio` within the code, because Snakemake with Conda ensures that the required tools are installed and available.
Applied to files:
bio/mofa2/environment.yaml
📚 Learning: 2025-02-11T12:24:22.592Z
Learnt from: dlaehnemann
Repo: snakemake/snakemake-wrappers PR: 3648
File: bio/nanosim/simulator/environment.yaml:6-6
Timestamp: 2025-02-11T12:24:22.592Z
Learning: For bioconda packages like nanosim, dependencies like scikit-learn are managed through the bioconda recipe and don't need to be explicitly added to the environment.yaml file when the main package is listed as a dependency.
Applied to files:
bio/mofa2/environment.yaml
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: Summary
🔇 Additional comments (2)
bio/mofa2/environment.yaml (1)
1-4: LGTM - Channels are correctly configured.The channel order (conda-forge, bioconda, nodefaults) follows the recommended convention for Bioconda packages.
bio/mofa2/environment.linux-64.pin.txt (1)
1-268: LGTM - Standard explicit pin file for reproducibility.This auto-generated pin file correctly captures the resolved environment for linux-64, enabling reproducible builds. The key package versions align with
environment.yamlspecifications:
bioconductor-mofa2-1.16.0(line 268)mofapy2-0.7.2(line 178)r-arrow-22.0.0(line 257)
|
Any reason you keep the |
At first I deleted it because I thought it had been created entirely by my EDIT: It's also on the main branch here on Github. |
|
Sorry! I mean the |
|
Oh sorry, I must have missed it. It seems I only deleted |
|
It looks good to me! |
3 participants
This adds a minimal wrapper for MOFA2 under
bio/mofa2which trains a model with default values and writes the model to an HDF5 file.QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Tests
Chores / Packaging
Documentation
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