🐍 add aracne3 and viper modules

modules/nf-core/aracne3/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-base=4.3.1

modules/nf-core/aracne3/main.nf

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+process ARACNE3 {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "docker.io/papaemmelab/aracne3:v1.0.1"
+
+    input:
+    tuple val(meta), path(expression_matrix)
+    path regulators
+
+    output:
+    tuple val(meta), path("*${meta.id}.tsv"),   emit: consensus_network
+    tuple val(meta), path("subnets"),           emit: subnets
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    /ARACNe3/build/src/app/ARACNe3_app_release \\
+        -e $expression_matrix \\
+        -r $regulators \\
+        -o . \\
+        --runid $meta.id \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    cat <<-END_VERSIONS > versions.yml
+    /ARACNe3/build/src/app/ARACNe3_app_release \\
+        -e $expression_matrix \\
+        -r $regulators \\
+        -o . \\
+        --runid $meta.id \\
+        $args
+
+    END_VERSIONS
+    """
+}

modules/nf-core/aracne3/meta.yml

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+name: aracne3
+description: Run ARACNe3 for protein regulatory interactions inference tool
+keywords:
+  - ARACNe3
+  - RNA-seq
+  - Protein Activity
+  - Networks
+tools:
+  - aracne3:
+      description: >
+        ARACNe3 is an implementation of ARACNe which presents computational improvements
+        and theoretical changes to the recent ARACNe-AP implementation. Given a list of
+        regulators and a gene expression profile, ARACNe3 is used to infer irreducibly
+        dependent regulatory interactions and output a Gene Regulatory Network (GRN).
+        The mainstream analysis generates many GRNs of subsamples of the profile (called
+        "subnetworks") and then consolidates the subnetworks into a robust GRN. The
+        consolidated output is a GRN whose edge strengths can be quantified by several
+        statistical metrics.
+      homepage: https://github.com/califano-lab/ARACNe3
+      documentation: https://github.com/califano-lab/ARACNe3/blob/main/README.md
+      tool_dev_url: https://github.com/califano-lab/ARACNe3/tree/main
+      doi: 10.1093/bioinformatics/btw21
+
+input:
+  - - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+    - expression_matrix:
+          type: file
+          description: Normalized (TPM, CPM etc) gene expression matrix with genes as rows and samples as columns.
+          pattern: "*.tsv"
+  - - regulators:
+        type: file
+        description: List of genes (regulators) to be used for interactions network inference.
+        pattern: "*.txt"
+
+output:
+  - consensus_network:
+    - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+    - "consolidated-net_<runid>.tsv":
+        type: file
+        description: Consolidated Mutual Information estimation and significance per regulator/gene pair.
+        pattern: "consolidated-net_<runid>.tsv"
+
+  - subnets:
+    - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+    - "subnets":
+        type: directory
+        description: Mutual Information estimation per regulator/gene pair, per subnetwork generated.
+        pattern: "consolidated-net_<runid>.tsv"
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@stikos"
+  - "@ddomenico"
+  - "@juanesarango"
+maintainers:
+  - "@stikos"
+  - "@ddomenico"
+  - "@juanesarango"

modules/nf-core/aracne3/tests/main.nf.test

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+nextflow_process {
+
+    name "Test module ARACNE3"
+    script "../main.nf"
+    process "ARACNE3"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "aracne3"
+
+    test("aracne3_5samples_100regulators_5threads") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir = "./output"
+                aracne3_args = "--threads 5 --alpha 1 --seed 9001"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/aracne3/expression_matrix.tsv", checkIfExists: true),
+                ]
+                input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/aracne3/regulators.txt", checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.consensus_network.get(0).get(1)).match("tsv") },
+                { assert snapshot(process.out.subnets.get(0).get(1)).match(".tsv") },
+                { assert snapshot(process.out.versions).match("versions") },
+            )
+        }
+
+    }
+}

modules/nf-core/aracne3/tests/main.nf.test.snap

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+{
+    "versions": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-05-06T14:58:18.838692"
+    },
+    "tsv": {
+        "content": [
+            "consolidated-net_test.tsv:md5,6221a5778044ce418e893e1d62ca3da2"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-05-06T14:58:18.308379"
+    },
+    ".tsv": {
+        "content": [
+            [
+                "subnet1_test.tsv:md5,ebbae6bae8792a2d073735e1d86da69c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-05-06T14:58:18.519708"
+    }
+}

modules/nf-core/aracne3/tests/nextflow.config

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+docker.runOptions = '--entrypoint ""'
+docker.enabled = true
+
+process {
+    withName: ARACNE3 {
+        container = "papaemmelab/aracne3:v1.0.0"
+        ext.args = params.aracne3_args
+    }
+}

modules/nf-core/viper/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::bioconductor-viper=1.40.0"

modules/nf-core/viper/main.nf

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+process VIPER {
+    tag "$meta_exp.id vs $meta_net.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container 'papaemmelab/viper'
+
+    input:
+    tuple val(meta_net), path(network)
+    tuple val(meta_exp), path(expression_matrix)
+
+    output:
+    path "${meta_exp.id}_vs_${meta_net.id}.viper_matrix.tsv", emit: viper_matrix
+    path "versions.yml",                                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'viper.R'
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta_exp.id}_vs_${meta_net.id}"
+    """
+    touch ${prefix}.viper_matrix.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        viper: \$(Rscript -e "cat(as.character(packageVersion('viper')))"
+    END_VERSIONS
+    """
+}

modules/nf-core/viper/meta.yml

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+name: viper
+description: Run Virtual Inference of Protein-activity by Enriched Regulon analysis.
+keywords:
+  - Viper
+  - Regulators
+  - Protein Activity
+  - RNA-seq
+tools:
+  - viper:
+      description: |
+        The viper R package infers protein activity from gene expression data, 
+        and includes the VIPER and msVIPER algorithms developed by the Califano lab.
+      homepage: https://www.bioconductor.org/packages/release/bioc/html/viper.html
+      documentation: https://www.bioconductor.org/packages/release/bioc/vignettes/viper/inst/doc/viper.pdf
+      doi: 10.1038/ng.3593
+input:
+  - meta_net:
+      type: map
+      description: |
+        Groovy Map containing network information
+        e.g. `[ id:'network1' ]`
+  - network:
+        type: file
+        description: 3 column ARACNe network file.
+        pattern: "*.tsv"
+  - meta_exp:
+      type: map
+      description: |
+        Groovy Map containing expression matrix information
+        e.g. `[ id:'expression1' ]`
+  - expression_matrix:
+        type: file
+        description: Expression matrix with samples as columns and genes as rows.
+        pattern: "*.tsv"
+output:
+  - viper_matrix:
+      type: file
+      description: Viper output matrix of inferred protein activity.
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@ddomenico"
+  - "@juanesarango"
+  - "@stikos"
+maintainers:
+  - "@ddomenico"
+  - "@juanesarango"
+  - "@stikos"

modules/nf-core/viper/templates/viper.R

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+#!/usr/bin/env Rscript
+
+library(viper)
+
+# Inject variables
+exp_mat_file <- "${expression_matrix}"
+network_file <- "${network}"
+
+# Load regulon and expression matrix
+exp_mat <- as.matrix(read.table(exp_mat_file, header=TRUE))
+regul <- aracne2regulon(network_file, exp_mat)
+
+# Run VIPER
+vpres <- viper(exp_mat, regul, verbose = FALSE)
+
+# Output result
+output_file <- file.path("${meta_exp.id}_vs_${meta_net.id}.viper_matrix.tsv")
+write.table(vpres, file = output_file, sep = "\t", quote = FALSE)
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+viper_version <- as.character(packageVersion('viper'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    viper:', viper_version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################

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

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+nextflow_process {
+
+    name "Test Process VIPER"
+    script "../main.nf"
+    process "VIPER"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "viper"
+
+    test("test_viper") {
+
+        setup {
+            run("ARACNE3") {
+                script "../../aracne3/main.nf"
+                process {
+                """
+                input[0] = [ [id:"testexp"], file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/aracne3/expression_matrix.tsv', checkIfExists: true) ]
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/aracne3/regulators.txt', checkIfExists: true)
+                """
+                }
+            }
+        }
+
+        when {
+            params {
+                aracne3_args = "--threads 5 --alpha 1 --seed 9001"
+            }
+            process {
+                """
+                input[0] = ARACNE3.out.consensus_network.collect{ meta, consensus_network -> consensus_network }.map{ consensus_network -> [[ id: 'testnet'], consensus_network]}
+                input[1] = [ [id:"testexp"], file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/aracne3/expression_matrix.tsv', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.viper_matrix,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+}