new module: insitugame

modules/nf-core/insitugame/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::insitugame=1.0.6"

modules/nf-core/insitugame/main.nf

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+// Copyright (c) the nf-core community under an open-source MIT license.
+// See https://github.com/nf-core/modules for full license, file patching instructions and upstream contributing.
+
+process INSITUGAME {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/insitugame:1.0.6--pyhdfd78af_0':
+        'quay.io/biocontainers/insitugame:1.0.6--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(spatial_data)
+
+    output:
+    tuple val(meta), path("*.png") , emit: figures, optional: true
+    tuple val(meta), path("*.json"), emit: results
+    tuple val(meta), path("*.csv") , emit: tables
+    tuple val("${task.process}"), val('insitugame'), eval("python -c \"import importlib.metadata; print(importlib.metadata.version('insitugame'))\""), topic: versions, emit: versions_insitugame
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    python -c "
+import insitugame
+from insitugame import InSituGameAssay
+import pandas as pd
+import json
+
+df_in = pd.read_csv('${spatial_data}', sep=None, engine='python')
+cols = list(df_in.columns)
+
+sensitive = [cols[1]] if len(cols) > 1 else ['Sensitive']
+resistant = [cols[2]] if len(cols) > 2 else ['Resistant']
+stroma    = [cols[3]] if len(cols) > 3 else ['Stroma']
+
+gene_spec = {
+    'Sensitive': sensitive,
+    'Resistant': resistant,
+    'Stroma': stroma
+}
+assay = InSituGameAssay(gene_spec)
+
+results = {
+    'sample_id': '${prefix}',
+    'version': insitugame.__version__,
+    'status': 'completed',
+    'gene_spec': gene_spec,
+    'n_rows': len(df_in)
+}
+
+with open('${prefix}_results.json', 'w') as f:
+    json.dump(results, f, indent=2)
+
+df_out = pd.DataFrame([{'sample': '${prefix}', 'status': 'completed', 'n_rows': len(df_in)}])
+df_out.to_csv('${prefix}_tables.csv', index=False)
+"
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_results.json
+    touch ${prefix}_tables.csv
+    touch ${prefix}_figure.png
+    """
+}

modules/nf-core/insitugame/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "insitugame"
+description: "In situ spatial evolutionary game assay for inferring tumor subclonal payoff matrices and adaptive therapy regimens from intact spatial transcriptomics."
+keywords:
+  - spatial transcriptomics
+  - evolutionary game theory
+  - oncology
+  - cancer
+  - visium
+tools:
+  - "insitugame":
+      description: "Computational oncology assay for subclonal payoff matrices and evolutionary game dynamics from spatial transcriptomics."
+      homepage: "https://lukecele.github.io/spatial-game-assay/"
+      documentation: "https://github.com/Lukecele/spatial-game-assay#readme"
+      tool_dev_url: "https://github.com/Lukecele/spatial-game-assay"
+      doi: "10.5281/zenodo.23585216"
+      licence:
+        - "GPL-3.0-or-later"
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - spatial_data:
+        type: file
+        description: Spatial transcriptomics counts and coordinate table
+        pattern: "*.{tsv,csv,tsv.gz,csv.gz,h5ad}"
+
+output:
+  figures:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.png":
+          type: file
+          description: Spatial payoff simplex and subclonal interaction figures
+          pattern: "*.png"
+  results:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.json":
+          type: file
+          description: Inferred payoff matrices and Nash equilibria in JSON format
+          pattern: "*.json"
+  tables:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.csv":
+          type: file
+          description: Inferred game payoff matrix and spot metrics table
+          pattern: "*.csv"
+  versions_insitugame:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "insitugame":
+          type: string
+          description: The name of the tool
+      - 'python -c "import importlib.metadata; print(importlib.metadata.version(''insitugame''))"':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - insitugame:
+          type: string
+          description: The name of the tool
+      - python -c "import importlib.metadata; print(importlib.metadata.version('insitugame'))":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Lukecele"
+maintainers:
+  - "@Lukecele"

modules/nf-core/insitugame/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process INSITUGAME"
+    script "../main.nf"
+    process "INSITUGAME"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "insitugame"
+
+    test("spatial - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.results,
+                    process.out.tables,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("spatial - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/insitugame/tests/main.nf.test.snap

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+{
+    "spatial - tsv": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test_results.json:md5,3d48992b2e604a84a90293fc50304a6b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test_tables.csv:md5,4603676b8ed90a50dbade6c13473df60"
+                ]
+            ],
+            {
+                "versions_insitugame": [
+                    [
+                        "INSITUGAME",
+                        "insitugame",
+                        "1.0.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-10-27T13:51:53.446431902",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "spatial - tsv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tables.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        "INSITUGAME",
+                        "insitugame",
+                        "1.0.6"
+                    ]
+                ],
+                "figures": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_figure.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_results.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tables": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_tables.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_insitugame": [
+                    [
+                        "INSITUGAME",
+                        "insitugame",
+                        "1.0.6"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-10-27T13:50:33.499103589",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    }
+}

modules/nf-core/insitugame/tests/tags.yml

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+insitugame:
+  - modules/nf-core/insitugame/**