From 1f1e708a507870fa3dd891c8f68d37b182874ff4 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Thu, 12 Feb 2026 13:51:03 +0100
Subject: [PATCH 01/10] New module: cosimflow for cosine similarity

---
 modules/nf-core/cosimflow/environment.yml    |  13 +++
 modules/nf-core/cosimflow/main.nf            | 114 +++++++++++++++++++
 modules/nf-core/cosimflow/meta.yml           |  56 +++++++++
 modules/nf-core/cosimflow/tests/main.nf.test |  42 +++++++
 4 files changed, 225 insertions(+)
 create mode 100644 modules/nf-core/cosimflow/environment.yml
 create mode 100644 modules/nf-core/cosimflow/main.nf
 create mode 100644 modules/nf-core/cosimflow/meta.yml
 create mode 100644 modules/nf-core/cosimflow/tests/main.nf.test

diff --git a/modules/nf-core/cosimflow/environment.yml b/modules/nf-core/cosimflow/environment.yml
new file mode 100644
index 000000000000..0581255153cc
--- /dev/null
+++ b/modules/nf-core/cosimflow/environment.yml
@@ -0,0 +1,13 @@
+name: cosimflow
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-base
+  - r-lsa
+  - r-pheatmap
+  - r-optparse
+  - r-readr
+  - r-readxl
+  - r-dplyr
diff --git a/modules/nf-core/cosimflow/main.nf b/modules/nf-core/cosimflow/main.nf
new file mode 100644
index 000000000000..ba2a6e3a4b53
--- /dev/null
+++ b/modules/nf-core/cosimflow/main.nf
@@ -0,0 +1,114 @@
+process COSIMFLOW {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0d94018089:00bd7e543b7135f299839496732948679f2e3073-0' :
+        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0d94018089:00bd7e543b7135f299839496732948679f2e3073-0' }"
+
+    input:
+    tuple val(meta), path(expression_matrix)
+
+    output:
+    tuple val(meta), path("*_matrix.csv") , emit: matrix
+    tuple val(meta), path("*_heatmap.png"), emit: heatmap
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    #!/usr/bin/env Rscript
+
+    suppressPackageStartupMessages({
+        library(optparse)
+        library(readr)
+        library(readxl)
+        library(dplyr)
+        library(lsa)
+        library(pheatmap)
+    })
+
+    option_list = list(
+        make_option(c("-i","--input"), type="character", help="Input file"),
+        make_option(c("-o","--out_prefix"), type="character", default="cosine"),
+        make_option(c("-m","--method"), type="character", default="cosine"),
+        make_option(c("-g","--min_gene_mean"), type="double", default=0.0),
+        make_option(c("-s","--sample_cols"), type="character", default="auto")
+    )
+
+    # AQUÍ PASAMOS LOS ARGUMENTOS DE NEXTFLOW DIRECTAMENTE
+    args_list <- c("--input", "$expression_matrix", "--out_prefix", "$prefix")
+    
+    # Añadimos los argumentos extra si existen
+    extra_args <- "$args"
+    if (nchar(extra_args) > 0) {
+        args_list <- c(args_list, unlist(strsplit(extra_args, "\\\\s+")))
+    }
+
+    opt <- parse_args(OptionParser(option_list=option_list), args=args_list)
+
+    # ---- Load table ----
+    if (grepl("\\\\.xlsx?\$", opt\$input, ignore.case=TRUE)) {
+        df <- as.data.frame(read_excel(opt\$input))
+    } else {
+        df <- as.data.frame(read_csv(opt\$input, col_types = cols(.default = col_guess())))
+    }
+
+    # ---- Set rownames ----
+    first_col <- names(df)[1]
+    if (tolower(first_col) %in% c("gene","id", "gene_id")) {
+        if (is.character(df[[first_col]]) || is.factor(df[[first_col]])) {
+            rownames(df) <- df[[first_col]]
+            df[[first_col]] <- NULL
+        }
+    }
+
+    # ---- Select sample columns ----
+    if (opt\$sample_cols != "auto") {
+        cols <- trimws(unlist(strsplit(opt\$sample_cols,",")))
+        mat <- as.matrix(df[, cols, drop=FALSE])
+    } else {
+        num_cols <- sapply(df, is.numeric)
+        mat <- as.matrix(df[, num_cols, drop=FALSE])
+    }
+
+    # ---- Filter ----
+    if (opt\$min_gene_mean > 0) {
+        keep <- rowMeans(mat, na.rm=TRUE) >= opt\$min_gene_mean
+        mat <- mat[keep, , drop=FALSE]
+    }
+
+    # ---- Compute ----
+    method <- tolower(opt\$method)
+    if (method == "cosine") {
+        sim <- lsa::cosine(mat)
+    } else {
+        sim <- cor(mat, method = method, use = "pairwise.complete.obs")
+    }
+
+    colnames(sim) <- colnames(mat)
+    rownames(sim) <- colnames(mat)
+
+    # ---- Save ----
+    write.csv(sim, paste0(opt\$out_prefix, "_matrix.csv"), quote=FALSE, row.names=TRUE)
+
+    png(paste0(opt\$out_prefix, "_heatmap.png"), width=900, height=700)
+    pheatmap(sim, display_numbers=TRUE, cluster_rows=FALSE, cluster_cols=FALSE)
+    dev.off()
+
+    # ---- Versions ----
+    r_version <- paste0(R.version\$major, ".", R.version\$minor)
+    writeLines(c(
+        "\\"${task.process}\\":",
+        paste0("    r-base: ", r_version),
+        paste0("    r-lsa: ", packageVersion("lsa")),
+        paste0("    r-pheatmap: ", packageVersion("pheatmap"))
+    ), "versions.yml")
+    """
+}
diff --git a/modules/nf-core/cosimflow/meta.yml b/modules/nf-core/cosimflow/meta.yml
new file mode 100644
index 000000000000..884d5b2419aa
--- /dev/null
+++ b/modules/nf-core/cosimflow/meta.yml
@@ -0,0 +1,56 @@
+name: "cosimflow"
+description: Calculates the cosine similarity matrix between samples based on a gene expression matrix.
+keywords:
+  - similarity
+  - cosine
+  - clustering
+  - rnaseq
+  - heatmap
+tools:
+  - "r":
+      description: "R is a free software environment for statistical computing and graphics."
+      homepage: "https://www.r-project.org/"
+      documentation: "https://cran.r-project.org/manuals.html"
+      tool_dev_url: "https://github.com/miguelrosell/nf-cosimflow"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information, e.g. [ id:'test' ].
+    - expression_matrix:
+        type: file
+        description: |
+          CSV or XLSX file containing the expression matrix. 
+          Rows should be features (genes) and columns should be samples.
+          First column must be gene IDs.
+        pattern: "*.{csv,xlsx}"
+
+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 cosine similarity scores (0-1).
+          pattern: "*_matrix.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 cosine similarity matrix as a heatmap.
+          pattern: "*_heatmap.png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions.
+          pattern: "versions.yml"
+
+authors:
+  - "@miguelrosell"
diff --git a/modules/nf-core/cosimflow/tests/main.nf.test b/modules/nf-core/cosimflow/tests/main.nf.test
new file mode 100644
index 000000000000..ae0e68088992
--- /dev/null
+++ b/modules/nf-core/cosimflow/tests/main.nf.test
@@ -0,0 +1,42 @@
+nextflow_process {
+
+    name "Test Process COSIMFLOW"
+    script "../main.nf"
+    process "COSIMFLOW"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cosimflow"
+
+    test("Should run successfully with a simple CSV") {
+
+        when {
+            process {
+                """
+                // 1. Creamos un CSV dummy al vuelo para el test
+                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'''
+                
+                // 2. Definimos el input: [ meta, archivo ]
+                input[0] = [ [id:'test_sample'], test_csv ]
+                """
+            }
+        }
+
+        then {
+            // 3. Verificamos que termine con éxito
+            assert process.success
+            
+            // 4. Verificamos que se generen los archivos
+            assert process.out.matrix
+            assert process.out.heatmap
+            assert process.out.versions
+        }
+
+    }
+
+}

From 7c119563d434962c781664f4edca094700e8b8a3 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 13 Feb 2026 01:22:40 +0100
Subject: [PATCH 02/10] Refactor module: Rename to lsa/cosine, update deps, add
 stub and snapshots

---
 modules/nf-core/cosimflow/environment.yml     |  13 --
 modules/nf-core/cosimflow/main.nf             | 114 ------------------
 modules/nf-core/lsa/cosine/environment.yml    |  13 ++
 modules/nf-core/lsa/cosine/main.nf            |  41 +++++++
 .../{cosimflow => lsa/cosine}/meta.yml        |  30 +++--
 modules/nf-core/lsa/cosine/templates/cosine.R |  83 +++++++++++++
 .../cosine}/tests/main.nf.test                |   0
 tests/modules/nf-core/lsa/cosine/main.nf.test |  63 ++++++++++
 8 files changed, 218 insertions(+), 139 deletions(-)
 delete mode 100644 modules/nf-core/cosimflow/environment.yml
 delete mode 100644 modules/nf-core/cosimflow/main.nf
 create mode 100644 modules/nf-core/lsa/cosine/environment.yml
 create mode 100644 modules/nf-core/lsa/cosine/main.nf
 rename modules/nf-core/{cosimflow => lsa/cosine}/meta.yml (59%)
 create mode 100644 modules/nf-core/lsa/cosine/templates/cosine.R
 rename modules/nf-core/{cosimflow => lsa/cosine}/tests/main.nf.test (100%)
 create mode 100644 tests/modules/nf-core/lsa/cosine/main.nf.test

diff --git a/modules/nf-core/cosimflow/environment.yml b/modules/nf-core/cosimflow/environment.yml
deleted file mode 100644
index 0581255153cc..000000000000
--- a/modules/nf-core/cosimflow/environment.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-name: cosimflow
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - r-base
-  - r-lsa
-  - r-pheatmap
-  - r-optparse
-  - r-readr
-  - r-readxl
-  - r-dplyr
diff --git a/modules/nf-core/cosimflow/main.nf b/modules/nf-core/cosimflow/main.nf
deleted file mode 100644
index ba2a6e3a4b53..000000000000
--- a/modules/nf-core/cosimflow/main.nf
+++ /dev/null
@@ -1,114 +0,0 @@
-process COSIMFLOW {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0d94018089:00bd7e543b7135f299839496732948679f2e3073-0' :
-        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0d94018089:00bd7e543b7135f299839496732948679f2e3073-0' }"
-
-    input:
-    tuple val(meta), path(expression_matrix)
-
-    output:
-    tuple val(meta), path("*_matrix.csv") , emit: matrix
-    tuple val(meta), path("*_heatmap.png"), emit: heatmap
-    path "versions.yml"                   , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    
-    """
-    #!/usr/bin/env Rscript
-
-    suppressPackageStartupMessages({
-        library(optparse)
-        library(readr)
-        library(readxl)
-        library(dplyr)
-        library(lsa)
-        library(pheatmap)
-    })
-
-    option_list = list(
-        make_option(c("-i","--input"), type="character", help="Input file"),
-        make_option(c("-o","--out_prefix"), type="character", default="cosine"),
-        make_option(c("-m","--method"), type="character", default="cosine"),
-        make_option(c("-g","--min_gene_mean"), type="double", default=0.0),
-        make_option(c("-s","--sample_cols"), type="character", default="auto")
-    )
-
-    # AQUÍ PASAMOS LOS ARGUMENTOS DE NEXTFLOW DIRECTAMENTE
-    args_list <- c("--input", "$expression_matrix", "--out_prefix", "$prefix")
-    
-    # Añadimos los argumentos extra si existen
-    extra_args <- "$args"
-    if (nchar(extra_args) > 0) {
-        args_list <- c(args_list, unlist(strsplit(extra_args, "\\\\s+")))
-    }
-
-    opt <- parse_args(OptionParser(option_list=option_list), args=args_list)
-
-    # ---- Load table ----
-    if (grepl("\\\\.xlsx?\$", opt\$input, ignore.case=TRUE)) {
-        df <- as.data.frame(read_excel(opt\$input))
-    } else {
-        df <- as.data.frame(read_csv(opt\$input, col_types = cols(.default = col_guess())))
-    }
-
-    # ---- Set rownames ----
-    first_col <- names(df)[1]
-    if (tolower(first_col) %in% c("gene","id", "gene_id")) {
-        if (is.character(df[[first_col]]) || is.factor(df[[first_col]])) {
-            rownames(df) <- df[[first_col]]
-            df[[first_col]] <- NULL
-        }
-    }
-
-    # ---- Select sample columns ----
-    if (opt\$sample_cols != "auto") {
-        cols <- trimws(unlist(strsplit(opt\$sample_cols,",")))
-        mat <- as.matrix(df[, cols, drop=FALSE])
-    } else {
-        num_cols <- sapply(df, is.numeric)
-        mat <- as.matrix(df[, num_cols, drop=FALSE])
-    }
-
-    # ---- Filter ----
-    if (opt\$min_gene_mean > 0) {
-        keep <- rowMeans(mat, na.rm=TRUE) >= opt\$min_gene_mean
-        mat <- mat[keep, , drop=FALSE]
-    }
-
-    # ---- Compute ----
-    method <- tolower(opt\$method)
-    if (method == "cosine") {
-        sim <- lsa::cosine(mat)
-    } else {
-        sim <- cor(mat, method = method, use = "pairwise.complete.obs")
-    }
-
-    colnames(sim) <- colnames(mat)
-    rownames(sim) <- colnames(mat)
-
-    # ---- Save ----
-    write.csv(sim, paste0(opt\$out_prefix, "_matrix.csv"), quote=FALSE, row.names=TRUE)
-
-    png(paste0(opt\$out_prefix, "_heatmap.png"), width=900, height=700)
-    pheatmap(sim, display_numbers=TRUE, cluster_rows=FALSE, cluster_cols=FALSE)
-    dev.off()
-
-    # ---- Versions ----
-    r_version <- paste0(R.version\$major, ".", R.version\$minor)
-    writeLines(c(
-        "\\"${task.process}\\":",
-        paste0("    r-base: ", r_version),
-        paste0("    r-lsa: ", packageVersion("lsa")),
-        paste0("    r-pheatmap: ", packageVersion("pheatmap"))
-    ), "versions.yml")
-    """
-}
diff --git a/modules/nf-core/lsa/cosine/environment.yml b/modules/nf-core/lsa/cosine/environment.yml
new file mode 100644
index 000000000000..3b26d2dcaa0a
--- /dev/null
+++ b/modules/nf-core/lsa/cosine/environment.yml
@@ -0,0 +1,13 @@
+---
+name: lsa_cosine
+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
+  - conda-forge::r-readxl=1.4.5
+  - conda-forge::r-dplyr=1.2.0
diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
new file mode 100644
index 000000000000..8d3d4b4d37c9
--- /dev/null
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -0,0 +1,41 @@
+process LSA_COSINE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // Contenedores nuevos generados por el revisor
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4d94f159b95315adf8bf54fdc9db88db10a5aef72dca6245dd163b91e9e0437e/data' :
+        'community.wave.seqera.io/library/r-base_r-lsa_r-pheatmap_r-optparse_pruned:901156bc11e60b28' }"
+
+    input:
+    tuple val(meta), path(expression_matrix)
+
+    output:
+    tuple val(meta), path("*_matrix.csv") , emit: matrix
+    tuple val(meta), path("*_heatmap.png"), emit: heatmap
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    template 'cosine.R'
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_matrix.csv
+    touch ${prefix}_heatmap.png
+    
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(R --version | sed -n 1p | sed 's/R version //g' | sed 's/ (.*//g')
+        r-lsa: 0.73.3
+        r-pheatmap: 1.0.12
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/cosimflow/meta.yml b/modules/nf-core/lsa/cosine/meta.yml
similarity index 59%
rename from modules/nf-core/cosimflow/meta.yml
rename to modules/nf-core/lsa/cosine/meta.yml
index 884d5b2419aa..03954a9a1cfc 100644
--- a/modules/nf-core/cosimflow/meta.yml
+++ b/modules/nf-core/lsa/cosine/meta.yml
@@ -1,4 +1,5 @@
-name: "cosimflow"
+# name matches directory structure
+name: "lsa_cosine"
 description: Calculates the cosine similarity matrix between samples based on a gene expression matrix.
 keywords:
   - similarity
@@ -7,12 +8,16 @@ keywords:
   - rnaseq
   - heatmap
 tools:
-  - "r":
-      description: "R is a free software environment for statistical computing and graphics."
-      homepage: "https://www.r-project.org/"
-      documentation: "https://cran.r-project.org/manuals.html"
-      tool_dev_url: "https://github.com/miguelrosell/nf-cosimflow"
-      licence: ["MIT"]
+  - "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"]
+  - "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"]
 
 input:
   - - meta:
@@ -22,10 +27,9 @@ input:
     - expression_matrix:
         type: file
         description: |
-          CSV or XLSX file containing the expression matrix. 
+          CSV file containing the expression matrix. 
           Rows should be features (genes) and columns should be samples.
-          First column must be gene IDs.
-        pattern: "*.{csv,xlsx}"
+        pattern: "*.csv"
 
 output:
   - matrix:
@@ -35,7 +39,7 @@ output:
             Groovy Map containing sample information, e.g. [ id:'test' ].
       - "*_matrix.csv":
           type: file
-          description: A square matrix (CSV) containing pairwise cosine similarity scores (0-1).
+          description: A square matrix (CSV) containing pairwise similarity scores.
           pattern: "*_matrix.csv"
   - heatmap:
       - meta:
@@ -44,7 +48,7 @@ output:
             Groovy Map containing sample information, e.g. [ id:'test' ].
       - "*_heatmap.png":
           type: file
-          description: A PNG image visualizing the cosine similarity matrix as a heatmap.
+          description: A PNG image visualizing the similarity matrix as a heatmap.
           pattern: "*_heatmap.png"
   - versions:
       - versions.yml:
@@ -54,3 +58,5 @@ output:
 
 authors:
   - "@miguelrosell"
+maintainers:
+  - "@miguelrosell"
diff --git a/modules/nf-core/lsa/cosine/templates/cosine.R b/modules/nf-core/lsa/cosine/templates/cosine.R
new file mode 100644
index 000000000000..3f3f46fcb421
--- /dev/null
+++ b/modules/nf-core/lsa/cosine/templates/cosine.R
@@ -0,0 +1,83 @@
+#!/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"
+)
diff --git a/modules/nf-core/cosimflow/tests/main.nf.test b/modules/nf-core/lsa/cosine/tests/main.nf.test
similarity index 100%
rename from modules/nf-core/cosimflow/tests/main.nf.test
rename to modules/nf-core/lsa/cosine/tests/main.nf.test
diff --git a/tests/modules/nf-core/lsa/cosine/main.nf.test b/tests/modules/nf-core/lsa/cosine/main.nf.test
new file mode 100644
index 000000000000..c7134596a4ee
--- /dev/null
+++ b/tests/modules/nf-core/lsa/cosine/main.nf.test
@@ -0,0 +1,63 @@
+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()
+        }
+    }
+
+}

From 3294995fb1b7bb0a7872d649f6d5847705aabd41 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 13 Feb 2026 01:58:01 +0100
Subject: [PATCH 03/10] Fix: remove duplicate tests folder inside module
 directory

---
 modules/nf-core/lsa/cosine/tests/main.nf.test | 42 -------------------
 1 file changed, 42 deletions(-)
 delete mode 100644 modules/nf-core/lsa/cosine/tests/main.nf.test

diff --git a/modules/nf-core/lsa/cosine/tests/main.nf.test b/modules/nf-core/lsa/cosine/tests/main.nf.test
deleted file mode 100644
index ae0e68088992..000000000000
--- a/modules/nf-core/lsa/cosine/tests/main.nf.test
+++ /dev/null
@@ -1,42 +0,0 @@
-nextflow_process {
-
-    name "Test Process COSIMFLOW"
-    script "../main.nf"
-    process "COSIMFLOW"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "cosimflow"
-
-    test("Should run successfully with a simple CSV") {
-
-        when {
-            process {
-                """
-                // 1. Creamos un CSV dummy al vuelo para el test
-                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'''
-                
-                // 2. Definimos el input: [ meta, archivo ]
-                input[0] = [ [id:'test_sample'], test_csv ]
-                """
-            }
-        }
-
-        then {
-            // 3. Verificamos que termine con éxito
-            assert process.success
-            
-            // 4. Verificamos que se generen los archivos
-            assert process.out.matrix
-            assert process.out.heatmap
-            assert process.out.versions
-        }
-
-    }
-
-}

From a1dca67d5731e598046607ff17f7989361f58081 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 13 Feb 2026 02:28:21 +0100
Subject: [PATCH 04/10] Fix: remove 'def' from script variables so that
 template can access them

---
 modules/nf-core/lsa/cosine/main.nf            |  8 +--
 .../nf-core/lsa/cosine/tests}/main.nf.test    |  0
 .../lsa/cosine/tests/main.nf.test.snap        | 72 +++++++++++++++++++
 3 files changed, 76 insertions(+), 4 deletions(-)
 rename {tests/modules/nf-core/lsa/cosine => modules/nf-core/lsa/cosine/tests}/main.nf.test (100%)
 create mode 100644 modules/nf-core/lsa/cosine/tests/main.nf.test.snap

diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
index 8d3d4b4d37c9..0c4008d732d4 100644
--- a/modules/nf-core/lsa/cosine/main.nf
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -2,7 +2,6 @@ process LSA_COSINE {
     tag "$meta.id"
     label 'process_medium'
 
-    // Contenedores nuevos generados por el revisor
     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' :
@@ -14,14 +13,15 @@ process LSA_COSINE {
     output:
     tuple val(meta), path("*_matrix.csv") , emit: matrix
     tuple val(meta), path("*_heatmap.png"), emit: heatmap
-    path "versions.yml"                   , emit: versions
+    path "versions.yml" , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    // HEMOS QUITADO EL 'def' DE AQUÍ ABAJO PARA QUE LA PLANTILLA LO VEA
+    args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
     template 'cosine.R'
 
     stub:
diff --git a/tests/modules/nf-core/lsa/cosine/main.nf.test b/modules/nf-core/lsa/cosine/tests/main.nf.test
similarity index 100%
rename from tests/modules/nf-core/lsa/cosine/main.nf.test
rename to modules/nf-core/lsa/cosine/tests/main.nf.test
diff --git a/modules/nf-core/lsa/cosine/tests/main.nf.test.snap b/modules/nf-core/lsa/cosine/tests/main.nf.test.snap
new file mode 100644
index 000000000000..93cf015c5f23
--- /dev/null
+++ b/modules/nf-core/lsa/cosine/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "Stub run": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_matrix.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_heatmap.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,ccaf13b49437e0a66e949615becf4292"
+                ],
+                "heatmap": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_heatmap.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        "test_sample_matrix.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ccaf13b49437e0a66e949615becf4292"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2026-02-13T02:14:38.341084051"
+    },
+    "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"
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
+        },
+        "timestamp": "2026-02-13T02:24:53.88495333"
+    }
+}
\ No newline at end of file

From a52a2b6f3a155f3ae82e9819b11284e2e4d08017 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 13 Feb 2026 02:52:08 +0100
Subject: [PATCH 05/10] Fix: removing Spanish comment

---
 modules/nf-core/lsa/cosine/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
index 0c4008d732d4..2dba59c45e22 100644
--- a/modules/nf-core/lsa/cosine/main.nf
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -19,7 +19,6 @@ process LSA_COSINE {
     task.ext.when == null || task.ext.when
 
     script:
-    // HEMOS QUITADO EL 'def' DE AQUÍ ABAJO PARA QUE LA PLANTILLA LO VEA
     args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     template 'cosine.R'

From fdffc3c8dc1bb2b2c1b039786a9ba2255d2135eb Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 13 Feb 2026 14:25:49 +0100
Subject: [PATCH 06/10] Fix: removed unused dependencies and use dynamic
 versioning in stub

---
 modules/nf-core/lsa/cosine/environment.yml |  2 --
 modules/nf-core/lsa/cosine/main.nf         | 10 +++++-----
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/lsa/cosine/environment.yml b/modules/nf-core/lsa/cosine/environment.yml
index 3b26d2dcaa0a..6ef0aff9fbc4 100644
--- a/modules/nf-core/lsa/cosine/environment.yml
+++ b/modules/nf-core/lsa/cosine/environment.yml
@@ -9,5 +9,3 @@ dependencies:
   - conda-forge::r-pheatmap=1.0.13
   - conda-forge::r-optparse=1.7.5
   - conda-forge::r-readr=2.1.6
-  - conda-forge::r-readxl=1.4.5
-  - conda-forge::r-dplyr=1.2.0
diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
index 2dba59c45e22..661241c1cafd 100644
--- a/modules/nf-core/lsa/cosine/main.nf
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -13,7 +13,7 @@ process LSA_COSINE {
     output:
     tuple val(meta), path("*_matrix.csv") , emit: matrix
     tuple val(meta), path("*_heatmap.png"), emit: heatmap
-    path "versions.yml" , emit: versions
+    path "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,8 +24,8 @@ process LSA_COSINE {
     template 'cosine.R'
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_matrix.csv
     touch ${prefix}_heatmap.png
@@ -33,8 +33,8 @@ process LSA_COSINE {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         r-base: \$(R --version | sed -n 1p | sed 's/R version //g' | sed 's/ (.*//g')
-        r-lsa: 0.73.3
-        r-pheatmap: 1.0.12
+        r-lsa: \$(Rscript -e "library(lsa); cat(as.character(packageVersion('lsa')))")
+        r-pheatmap: \$(Rscript -e "library(pheatmap); cat(as.character(packageVersion('pheatmap')))")
     END_VERSIONS
     """
 }

From 335a553cb7b3147a7539033996f2376ce1f7bd38 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 20 Feb 2026 15:56:52 +0100
Subject: [PATCH 07/10] Fix: linting errors, yaml structure, empty stubs, and
 updated snapshots

---
 modules/nf-core/lsa/cosine/environment.yml    |  1 -
 modules/nf-core/lsa/cosine/main.nf            |  4 ++--
 modules/nf-core/lsa/cosine/meta.yml           |  6 ++---
 modules/nf-core/lsa/cosine/tests/main.nf.test |  4 ++--
 .../lsa/cosine/tests/main.nf.test.snap        | 22 +++++++++----------
 5 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/modules/nf-core/lsa/cosine/environment.yml b/modules/nf-core/lsa/cosine/environment.yml
index 6ef0aff9fbc4..67fda59b5823 100644
--- a/modules/nf-core/lsa/cosine/environment.yml
+++ b/modules/nf-core/lsa/cosine/environment.yml
@@ -1,5 +1,4 @@
 ---
-name: lsa_cosine
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
index 661241c1cafd..ba242bd0da37 100644
--- a/modules/nf-core/lsa/cosine/main.nf
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -27,8 +27,8 @@ process LSA_COSINE {
     args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_matrix.csv
-    touch ${prefix}_heatmap.png
+    echo "dummy matrix data" >  ${prefix}_matrix.csv
+    echo "dummy matrix data" >  ${prefix}_heatmap.png
     
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/lsa/cosine/meta.yml b/modules/nf-core/lsa/cosine/meta.yml
index 03954a9a1cfc..236dff62c24a 100644
--- a/modules/nf-core/lsa/cosine/meta.yml
+++ b/modules/nf-core/lsa/cosine/meta.yml
@@ -33,7 +33,7 @@ input:
 
 output:
   - matrix:
-      - meta:
+      meta:
           type: map
           description: |
             Groovy Map containing sample information, e.g. [ id:'test' ].
@@ -42,7 +42,7 @@ output:
           description: A square matrix (CSV) containing pairwise similarity scores.
           pattern: "*_matrix.csv"
   - heatmap:
-      - meta:
+       meta:
           type: map
           description: |
             Groovy Map containing sample information, e.g. [ id:'test' ].
@@ -51,7 +51,7 @@ output:
           description: A PNG image visualizing the similarity matrix as a heatmap.
           pattern: "*_heatmap.png"
   - versions:
-      - versions.yml:
+       "versions.yml":
           type: file
           description: File containing software versions.
           pattern: "versions.yml"
diff --git a/modules/nf-core/lsa/cosine/tests/main.nf.test b/modules/nf-core/lsa/cosine/tests/main.nf.test
index c7134596a4ee..5210aa68513a 100644
--- a/modules/nf-core/lsa/cosine/tests/main.nf.test
+++ b/modules/nf-core/lsa/cosine/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
                 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 ]
                 """
             }
@@ -43,7 +43,7 @@ nextflow_process {
     // Test 2: Stub run (fast check)
     test("Stub run") {
         options "-stub"
-        
+
         when {
             process {
                 """
diff --git a/modules/nf-core/lsa/cosine/tests/main.nf.test.snap b/modules/nf-core/lsa/cosine/tests/main.nf.test.snap
index 93cf015c5f23..cb48832156a0 100644
--- a/modules/nf-core/lsa/cosine/tests/main.nf.test.snap
+++ b/modules/nf-core/lsa/cosine/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test_sample"
                         },
-                        "test_sample_matrix.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sample_matrix.csv:md5,3932b231a8a14016bc1e7a245f05246c"
                     ]
                 ],
                 "1": [
@@ -15,18 +15,18 @@
                         {
                             "id": "test_sample"
                         },
-                        "test_sample_heatmap.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sample_heatmap.png:md5,3932b231a8a14016bc1e7a245f05246c"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,ccaf13b49437e0a66e949615becf4292"
+                    "versions.yml:md5,b77351a76d91db12e57dd88f7e2e0184"
                 ],
                 "heatmap": [
                     [
                         {
                             "id": "test_sample"
                         },
-                        "test_sample_heatmap.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sample_heatmap.png:md5,3932b231a8a14016bc1e7a245f05246c"
                     ]
                 ],
                 "matrix": [
@@ -34,19 +34,19 @@
                         {
                             "id": "test_sample"
                         },
-                        "test_sample_matrix.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_sample_matrix.csv:md5,3932b231a8a14016bc1e7a245f05246c"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ccaf13b49437e0a66e949615becf4292"
+                    "versions.yml:md5,b77351a76d91db12e57dd88f7e2e0184"
                 ]
             }
         ],
+        "timestamp": "2026-02-20T15:51:35.612855607",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-02-13T02:14:38.341084051"
+        }
     },
     "Should run successfully with a simple CSV": {
         "content": [
@@ -63,10 +63,10 @@
             ],
             "test_sample_heatmap.png"
         ],
+        "timestamp": "2026-02-13T02:24:53.88495333",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.7"
-        },
-        "timestamp": "2026-02-13T02:24:53.88495333"
+        }
     }
 }
\ No newline at end of file

From dc20e9186ac1fa6679ab330fc9f626a1968d4866 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 20 Feb 2026 16:19:00 +0100
Subject: [PATCH 08/10] Fix: update meta.yml structure, keys and trailing
 whitespaces

---
 modules/nf-core/lsa/cosine/meta.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/lsa/cosine/meta.yml b/modules/nf-core/lsa/cosine/meta.yml
index 236dff62c24a..94895a286612 100644
--- a/modules/nf-core/lsa/cosine/meta.yml
+++ b/modules/nf-core/lsa/cosine/meta.yml
@@ -1,5 +1,5 @@
 # name matches directory structure
-name: "lsa_cosine"
+name: "lsa/cosine"
 description: Calculates the cosine similarity matrix between samples based on a gene expression matrix.
 keywords:
   - similarity
@@ -27,31 +27,31 @@ input:
     - expression_matrix:
         type: file
         description: |
-          CSV file containing the expression matrix. 
+          CSV file containing the expression matrix.
           Rows should be features (genes) and columns should be samples.
         pattern: "*.csv"
 
 output:
   - matrix:
-      meta:
+      - meta:
           type: map
           description: |
             Groovy Map containing sample information, e.g. [ id:'test' ].
-      - "*_matrix.csv":
+      - matrix:
           type: file
           description: A square matrix (CSV) containing pairwise similarity scores.
           pattern: "*_matrix.csv"
   - heatmap:
-       meta:
+      - meta:
           type: map
           description: |
             Groovy Map containing sample information, e.g. [ id:'test' ].
-      - "*_heatmap.png":
+      - heatmap:
           type: file
           description: A PNG image visualizing the similarity matrix as a heatmap.
           pattern: "*_heatmap.png"
   - versions:
-       "versions.yml":
+      - versions:
           type: file
           description: File containing software versions.
           pattern: "versions.yml"

From 6075c1a203a4529fad74f2ec83887278e9f1cde9 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 20 Feb 2026 16:33:25 +0100
Subject: [PATCH 09/10] Fix: strict nf-core schema for meta.yml outputs and
 remove trailing whitespace

---
 modules/nf-core/lsa/cosine/main.nf  |  2 +-
 modules/nf-core/lsa/cosine/meta.yml | 40 ++++++++++++++---------------
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/lsa/cosine/main.nf b/modules/nf-core/lsa/cosine/main.nf
index ba242bd0da37..adff29bf8021 100644
--- a/modules/nf-core/lsa/cosine/main.nf
+++ b/modules/nf-core/lsa/cosine/main.nf
@@ -29,7 +29,7 @@ process LSA_COSINE {
     """
     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')
diff --git a/modules/nf-core/lsa/cosine/meta.yml b/modules/nf-core/lsa/cosine/meta.yml
index 94895a286612..6a1d1fde0453 100644
--- a/modules/nf-core/lsa/cosine/meta.yml
+++ b/modules/nf-core/lsa/cosine/meta.yml
@@ -33,28 +33,28 @@ input:
 
 output:
   - matrix:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information, e.g. [ id:'test' ].
-      - matrix:
-          type: file
-          description: A square matrix (CSV) containing pairwise similarity scores.
-          pattern: "*_matrix.csv"
+      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"
   - heatmap:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information, e.g. [ id:'test' ].
-      - heatmap:
-          type: file
-          description: A PNG image visualizing the similarity matrix as a heatmap.
-          pattern: "*_heatmap.png"
+      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"
   - versions:
-      - versions:
-          type: file
-          description: File containing software versions.
-          pattern: "versions.yml"
+      "versions.yml":
+        type: file
+        description: File containing software versions.
+        pattern: "versions.yml"
 
 authors:
   - "@miguelrosell"

From 7cb29c7bff5d5fdb868e3ff03df75d01317e1340 Mon Sep 17 00:00:00 2001
From: miguelrosell <miguelnorty@gmail.com>
Date: Fri, 20 Feb 2026 16:55:20 +0100
Subject: [PATCH 10/10] Fix: correct process name and use lint --fix for
 matching output structure

---
 modules/nf-core/lsa/cosine/meta.yml | 55 +++++++++++++++++------------
 1 file changed, 32 insertions(+), 23 deletions(-)

diff --git a/modules/nf-core/lsa/cosine/meta.yml b/modules/nf-core/lsa/cosine/meta.yml
index 6a1d1fde0453..964cac6cd7de 100644
--- a/modules/nf-core/lsa/cosine/meta.yml
+++ b/modules/nf-core/lsa/cosine/meta.yml
@@ -1,6 +1,7 @@
 # name matches directory structure
-name: "lsa/cosine"
-description: Calculates the cosine similarity matrix between samples based on a gene expression matrix.
+name: "lsa_cosine"
+description: Calculates the cosine similarity matrix between samples based on a gene
+  expression matrix.
 keywords:
   - similarity
   - cosine
@@ -13,11 +14,13 @@ tools:
       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:
@@ -30,32 +33,38 @@ input:
           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"
-  - 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"
-  - versions:
-      "versions.yml":
+  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: