New module: lsa/cosine (calculate cosine similarity)

modules/nf-core/lsa/cosine/environment.yml

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+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-base=4.5.2
+  - conda-forge::r-lsa=0.73.4
+  - conda-forge::r-pheatmap=1.0.13
+  - conda-forge::r-optparse=1.7.5
+  - conda-forge::r-readr=2.1.6

modules/nf-core/lsa/cosine/main.nf

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+process LSA_COSINE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4d94f159b95315adf8bf54fdc9db88db10a5aef72dca6245dd163b91e9e0437e/data' :
+        'community.wave.seqera.io/library/r-base_r-lsa_r-pheatmap_r-optparse_pruned:901156bc11e60b28' }"
+
+    input:
+    tuple val(meta), path(expression_matrix)
+
+    output:
+    tuple val(meta), path("*_matrix.csv") , emit: matrix
+    tuple val(meta), path("*_heatmap.png"), emit: heatmap
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    template 'cosine.R'
+
+    stub:
+    args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "dummy matrix data" >  ${prefix}_matrix.csv
+    echo "dummy matrix data" >  ${prefix}_heatmap.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(R --version | sed -n 1p | sed 's/R version //g' | sed 's/ (.*//g')
+        r-lsa: \$(Rscript -e "library(lsa); cat(as.character(packageVersion('lsa')))")
+        r-pheatmap: \$(Rscript -e "library(pheatmap); cat(as.character(packageVersion('pheatmap')))")
+    END_VERSIONS
+    """
+}

modules/nf-core/lsa/cosine/meta.yml

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+# name matches directory structure
+name: "lsa_cosine"
+description: Calculates the cosine similarity matrix between samples based on a gene
+  expression matrix.
+keywords:
+  - similarity
+  - cosine
+  - clustering
+  - rnaseq
+  - heatmap
+tools:
+  - "lsa":
+      description: "Latent Semantic Analysis (LSA) package for R."
+      homepage: "https://cran.r-project.org/web/packages/lsa/index.html"
+      documentation: "https://cran.r-project.org/web/packages/lsa/lsa.pdf"
+      licence: ["GPL-2"]
+      identifier: ""
+  - "pheatmap":
+      description: "Pretty Heatmaps package for R."
+      homepage: "https://cran.r-project.org/web/packages/pheatmap/index.html"
+      documentation: "https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf"
+      licence: ["GPL-2"]
+      identifier: biotools:pheatmap
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information, e.g. [ id:'test' ].
+    - expression_matrix:
+        type: file
+        description: |
+          CSV file containing the expression matrix.
+          Rows should be features (genes) and columns should be samples.
+        pattern: "*.csv"
+        ontologies:
+          - edam: http://edamontology.org/format_3752 # CSV
+output:
+  matrix:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information, e.g. [ id:'test' ].
+      - "*_matrix.csv":
+          type: file
+          description: A square matrix (CSV) containing pairwise similarity scores.
+          pattern: "*_matrix.csv"
+          ontologies:
+            - edam: http://edamontology.org/format_3752 # CSV
+  heatmap:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information, e.g. [ id:'test' ].
+      - "*_heatmap.png":
+          type: file
+          description: A PNG image visualizing the similarity matrix as a heatmap.
+          pattern: "*_heatmap.png"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions.
+        pattern: "versions.yml"
+
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@miguelrosell"
+maintainers:
+  - "@miguelrosell"

modules/nf-core/lsa/cosine/templates/cosine.R

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+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages({
+  library(optparse)
+  library(readr)
+  library(lsa)
+  library(pheatmap)
+})
+
+# ---- Configurable options via task.ext.args ----
+option_list <- list(
+  make_option(c("-m", "--method"),
+    type = "character", default = "cosine",
+    help = "Similarity method: cosine, pearson, spearman"),
+  make_option(c("-g", "--min_gene_mean"),
+    type = "double", default = 0.0,
+    help = "Minimum gene mean expression filter")
+)
+
+opt <- parse_args(
+  OptionParser(option_list = option_list),
+  args = strsplit("$args", "[[:space:]]+")[[1]]
+)
+
+# ---- Load table ----
+df <- as.data.frame(
+  read_csv("${expression_matrix}",
+    col_types = cols(.default = col_guess()))
+)
+
+# ---- Set rownames from first column if character ----
+first_col <- names(df)[1]
+if (is.character(df[[first_col]]) || is.factor(df[[first_col]])) {
+  rownames(df) <- df[[first_col]]
+  df[[first_col]] <- NULL
+}
+
+# ---- Select numeric columns as the expression matrix ----
+mat <- as.matrix(
+  df[, sapply(df, is.numeric), drop = FALSE]
+)
+
+# ---- Filter low-expression genes ----
+if (opt\$min_gene_mean > 0) {
+  keep <- rowMeans(mat, na.rm = TRUE) >= opt\$min_gene_mean
+  mat <- mat[keep, , drop = FALSE]
+}
+
+# ---- Compute similarity ----
+if (opt\$method == "cosine") {
+  sim <- lsa::cosine(mat)
+} else {
+  sim <- cor(mat,
+    method = opt\$method, use = "pairwise.complete.obs")
+}
+colnames(sim) <- colnames(mat)
+rownames(sim) <- colnames(mat)
+
+# ---- Save matrix ----
+write.csv(sim, "${prefix}_matrix.csv",
+  quote = FALSE, row.names = TRUE)
+
+# ---- Save heatmap ----
+png("${prefix}_heatmap.png", width = 900, height = 700)
+pheatmap(sim,
+  display_numbers = TRUE,
+  cluster_rows = FALSE,
+  cluster_cols = FALSE)
+dev.off()
+
+# ---- Versions ----
+writeLines(
+  c(
+    '"${task.process}":',
+    paste("    r-base:",
+      paste0(R.version\$major, ".", R.version\$minor)),
+    paste("    r-lsa:",
+      as.character(packageVersion("lsa"))),
+    paste("    r-pheatmap:",
+      as.character(packageVersion("pheatmap")))
+  ),
+  "versions.yml"
+)

modules/nf-core/lsa/cosine/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process LSA_COSINE"
+    script "../main.nf"
+    process "LSA_COSINE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "lsa"
+    tag "lsa/cosine"
+
+    // Test 1: Real run
+    test("Should run successfully with a simple CSV") {
+
+        when {
+            process {
+                """
+                // Create dummy CSV
+                def test_csv = file("test_data.csv")
+                test_csv.text = '''gene_id,sample_A,sample_B,sample_C
+                GENE_1,10.0,10.5,0.0
+                GENE_2,50.0,50.5,2.0
+                GENE_3,0.0,0.0,100.0
+                GENE_4,100.0,99.5,10.0'''
+
+                input[0] = [ [id:'test_sample'], test_csv ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            // Snapshot versions and the matrix content (heatmap is binary, so we check name only)
+            assert snapshot(
+                process.out.matrix,
+                process.out.versions,
+                file(process.out.heatmap[0][1]).name
+            ).match()
+        }
+
+    }
+
+    // Test 2: Stub run (fast check)
+    test("Stub run") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                def test_csv = file("test_data.csv")
+                test_csv.text = '''gene_id,sample_A,sample_B''' // content doesn't matter for stub
+                input[0] = [ [id:'test_sample'], test_csv ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+}

modules/nf-core/lsa/cosine/tests/main.nf.test.snap

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+{
+    "Stub run": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_matrix.csv:md5,3932b231a8a14016bc1e7a245f05246c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_heatmap.png:md5,3932b231a8a14016bc1e7a245f05246c"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b77351a76d91db12e57dd88f7e2e0184"
+                ],
+                "heatmap": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_heatmap.png:md5,3932b231a8a14016bc1e7a245f05246c"
+                    ]
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_matrix.csv:md5,3932b231a8a14016bc1e7a245f05246c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b77351a76d91db12e57dd88f7e2e0184"
+                ]
+            }
+        ],
+        "timestamp": "2026-02-20T15:51:35.612855607",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.7"
+        }
+    },
+    "Should run successfully with a simple CSV": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_sample"
+                    },
+                    "test_sample_matrix.csv:md5,d84209a90c22f35ef4e6ea89a9d11770"
+                ]
+            ],
+            [
+                "versions.yml:md5,b77351a76d91db12e57dd88f7e2e0184"
+            ],
+            "test_sample_heatmap.png"
+        ],
+        "timestamp": "2026-02-13T02:24:53.88495333",
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
+        }
+    }
+}