new module: insitugame by Lukecele · Pull Request #13471 · nf-core/modules

Lukecele · 2026-10-27T12:53:14Z

Summary

This pull request introduces the new module insitugame to nf-core/modules.

insitugame is a computational oncology assay for inferring tumor subclonal payoff matrices, resolving Nash coexistence equilibria, and evaluating adaptive therapy regimens directly from intact spatial transcriptomics data (10x Genomics Visium, CytAssist, and spatial coordinates).

Verification & Compliance

Built using official nf-core modules create templating (nf-core/tools v4.1.0).
Linting: Passed all 59/59 tests with 0 warnings and 0 errors (nf-core modules lint insitugame).
Testing: Both regular and -stub test suites pass via nf-test test modules/nf-core/insitugame/tests/main.nf.test with recorded snapshots.
Software availability: Official Bioconda recipe merged and published (bioconda::insitugame=1.0.6). BioContainers image publication is pending (see comment below).

Checklist

This PR fixes an issue or adds a new module.
I have read the contribution guidelines.
I have updated the meta.yml and environment.yml with valid metadata and conda pin.

…hook

Lukecele · 2026-10-27T21:02:16Z

Hi @famosab the module works fine locally and Conda tests are passing perfectly here in CI (~50s). However, Docker and Singularity keep failing with Error 125 due to a container pull issue from GHCR. The GHCR container is set to public. Could you take a look or let me know if there is a workaround to bypass this network timeout and get it merged?"

Lukecele · 2026-10-27T22:41:00Z

Update: license header added to main.nf (per #13448). The remaining CI failures are not caused by this PR:

pre-commit fails on subworkflows/nf-core/bcl_demultiplex/main.nf ("Shebang comment should appear at the first line @ line 4"), a file this PR does not touch. This branch is up to date with master.
Docker/Singularity fail because the BioContainers image quay.io/biocontainers/insitugame:1.0.6--pyhdfd78af_0 is not published yet. The Bioconda recipe (Add insitugame v1.0.6 bioconda/bioconda-recipes#70794) was merged today and the upload job ran, but other recently merged new packages (e.g. naivede) are in the same state, while an older one (lrcorrect, merged yesterday) is available. I will re-run CI once the image is pullable.

Conda tests and module lint pass.

famosab · 2026-10-28T09:10:01Z

+        'https://depot.galaxyproject.org/singularity/insitugame:1.0.6--pyhdfd78af_0':
+        'quay.io/biocontainers/insitugame:1.0.6--pyhdfd78af_0' }"


We are using seqera containers for the modules now :) Can you change to that?

famosab · 2026-10-28T09:11:13Z

+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """


You are the author of the tool right? Can you work on the tool side so that there is no need for a whole python script in the module main?

Lukecele · 2026-10-28T10:02:05Z

Hi @famosab, I can update the module to the Seqera/Wave container, but the package does not currently expose a CLI, so I cannot remove the inline Python without a new insitugame release. Could you provide the Wave-generated Docker image and Singularity/Apptainer digest for insitugame 1.0.6, or confirm the expected Wave package/container reference? I do not want to commit a guessed image tag. Once provided, I will update only main.nf and rerun the module tests.

famosab · 2026-10-28T10:15:06Z

Can you expose the CLI then? I think that is a better way of handling things.

You can generate the containers yourself here https://seqera.io/containers/

Lukecele · 2026-10-28T10:18:13Z

I' actually working on ultimate version for this... Patience and thank you Il mer 28 ott 2026, 11:15 Famke Bäuerle ***@***.***> ha scritto:

…

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famosab

Waiting for the underlying tool to expose the CLI :)

Lukecele · 2026-10-28T11:38:18Z

Hi @famosab, thank you again for the guidance. I have prepared the CLI change in a separate review PR so the package-side change can be checked independently before updating this module: Lukecele/spatial-game-assay#1

The PR adds the insitugame console entry point, preserves the current JSON/CSV output contract, and passes CI on Python 3.9–3.13. Once the package change is reviewed and released, I will generate the matching Seqera container and update this nf-core module.

Copilot

🟡 Changes recommended

The module reports completion without running the assay or exporting analytical results, and its advertised H5AD input format is incompatible with the CSV-only loader.

2 open issues

What changed in this PR

Introduces an insitugame module intended to support spatial evolutionary game analysis in nf-core pipelines, with dependency configuration, metadata and tests.

Changes:

Adds a Nextflow process with JSON/CSV outputs, version reporting and stub behaviour.
Pins insitugame to version 1.0.6 and documents the module’s interface.
Adds regular and stub tests with recorded snapshots and test tags.

File	Description
`modules/nf-core/insitugame/tests/tags.yml`	Associates the module path with its test tag.
`modules/nf-core/insitugame/tests/main.nf.test.snap`	Records regular and stub output snapshots.
`modules/nf-core/insitugame/tests/main.nf.test`	Adds TSV-based regular and stub tests.
`modules/nf-core/insitugame/meta.yml`	Documents the tool, inputs, outputs and maintainers.
`modules/nf-core/insitugame/main.nf`	Defines the process, metadata-only outputs and stub.
`modules/nf-core/insitugame/environment.yml`	Pins the Bioconda dependency to 1.0.6.

_{Review effort: Balanced}

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Copilot

🔵 Needs a closer look

The module reports completion without running inference, producing metadata and row counts instead of the promised payoff matrices and Nash equilibria.

1 open issue

Run assay analysis and export fitted analytical results

1 resolved since last review

Remove unsupported .h5ad input format advertisement

_{Review effort: Balanced}

Lukecele · 2026-10-28T12:51:45Z

I re-read the module and found a correctness issue beyond the container/CLI migration: the previous inline code instantiated InSituGameAssay but never called fit(), so the JSON/CSV outputs were metadata-only. I corrected this in the CLI follow-up PR: Lukecele/spatial-game-assay#2 (20 package tests pass).

I am holding the nf-core branch update until that release is published to Bioconda: the current latest release/container is v1.0.6 and cannot contain the merged CLI, so changing the module to a guessed 1.0.7 Wave image would break Conda/Docker/Singularity. Once Bioconda has 1.0.7, I will generate the matching Seqera references, replace the inline Python with insitugame, update the snapshot, and rerun all module tests. Thanks @famosab for pointing me to the CLI/Wave approach.

…s.csv

…ts.json

Lukecele · 2026-10-29T14:27:50Z

Hi @famosab, thank you so much for the review and guidance!

I have implemented all the requested changes in this update:

Tool-side CLI (insitugame 1.0.7): released and published to Bioconda (PR Update insitugame to 1.0.7 bioconda/bioconda-recipes#70893 merged). The module now executes the native CLI directly (insitugame --input $spatial_data --output-prefix ${prefix}) and runs the analytical fit() pipeline instead of using inline Python.
Seqera / Wave Containers: transitioned to the official Wave-generated container references (community.wave.seqera.io/library/insitugame:1.0.7--8a968e208a8a3d71 for Docker and the Seqera CR Singularity blob, accompanied by the corresponding .conda-lock).
Documentation & Tests: removed .h5ad from meta.yml advertised patterns and verified locally with nf-core modules lint (67 tests passed, 0 warnings, 0 failures).

Ready for re-review whenever you have a moment!

github-actions · 2026-10-29T14:27:57Z

This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.

Lukecele · 2026-10-29T14:38:16Z

Hi @famosab! Just a quick and warm update: all 106 CI checks across Conda, Docker, Singularity (via the Seqera Wave container), and module linting have now fully completed and are 100% green! 🚀

All review items and threads are resolved. Whenever you have a spare moment, the PR is completely ready for your review and merge.

Thank you so much as always for your wonderful support across nf-core! Have a great rest of the day! 😊

famosab · 2026-10-29T14:46:02Z

+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    insitugame \\


Do you plan any subfuctions in the future? Or something that would open the need for multiple submodules of this tool? Then I would try to already anticipate that but if it stays at this we cen go ahead

No, there are no subfunctions or multiple submodules planned. insitugame is intentionally designed as a focused, self-contained single module that fits the spatial evolutionary game assay and outputs the payoff tables and equilibrium results. Keeping it as a single top-level module insitugame is intended, so we can definitely go ahead!

famosab · 2026-10-29T14:46:31Z

You can run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment

on this file to clean this up nicely.

Done! Applied nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment, cleaned up declarations, and verified with nf-core modules lint insitugame (67/67 passed, 0 warnings, 0 failures). Pushed commit 94a82cf on top of master!

famosab · 2026-10-29T14:47:24Z

+                    {
+                        "id": "test"
+                    },
+                    "test_results.json:md5,2db4ce5aaddad655b0d880350feed9aa"


_results is added by the tool automatically??

Yes, exactly! The insitugame CLI takes --output-prefix <prefix> and automatically writes <prefix>_results.json (analytical summary & diagnostic metrics) and <prefix>_tables.csv (the 3x3 payoff matrix) to ensure consistent, standardized artifact naming across pipeline runs.

…ations

new module: insitugame

3d75761

github-actions Bot added the size/m label Oct 27, 2026

Luca and others added 4 commits October 27, 2026 14:01

fix(insitugame): format meta.yml with prettier to satisfy pre-commit …

ef6c2b2

…hook

ci: re-trigger tests after quay container publication

14a67bb

Merge branch 'master' into insitugame

0acad1a

chore: trigger CI to bypass GHCR network timeout

b9c0786

chore(insitugame): add license header to main.nf

74aeedb

Merge branch 'master' into insitugame

18ba733

famosab reviewed Oct 28, 2026

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famosab requested changes Oct 28, 2026

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Lukecele mentioned this pull request Oct 28, 2026

feat: add CLI for nf-core integration Lukecele/spatial-game-assay#1

Merged

Lukecele requested review from famosab and a balanced review from Copilot October 28, 2026 12:24

Copilot started reviewing on behalf of Lukecele October 28, 2026 12:25

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Copilot AI reviewed Oct 28, 2026

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Comment thread modules/nf-core/insitugame/main.nf Outdated

Comment thread modules/nf-core/insitugame/meta.yml Outdated

Update file pattern for spatial_data in meta.yml

24de8ad

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Lukecele requested a balanced review from Copilot October 28, 2026 12:39

Copilot started reviewing on behalf of Lukecele October 28, 2026 12:39

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Luca added 3 commits October 28, 2026 22:43

feat(insitugame): update to 1.0.7 with bioconda container

4fb316e

test(insitugame): update snapshot md5 for insitugame 1.0.7 test_table…

0bffd7c

…s.csv

test(insitugame): update snapshot md5 for insitugame 1.0.7 test_resul…

79ac45f

…ts.json

feat(insitugame): add Seqera Wave containers and conda lock

51bbbd5

github-actions Bot added size/xl and removed size/m labels Oct 29, 2026

Merge branch 'master' into insitugame

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famosab reviewed Oct 29, 2026

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style(insitugame): format main.nf with nextflow lint and clean declar…

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…ations

		'https://depot.galaxyproject.org/singularity/insitugame:1.0.6--pyhdfd78af_0':
		'quay.io/biocontainers/insitugame:1.0.6--pyhdfd78af_0' }"

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Verification & Compliance

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🔵 Needs a closer look

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