new module: datavzrd

modules/nf-core/datavzrd/environment.yml

@@ -0,0 +1,7 @@
+name: datavzrd
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::datavzrd==2.36.12

modules/nf-core/datavzrd/main.nf

@@ -0,0 +1,63 @@
+process DATAVZRD {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/datavzrd:2.36.12--bb93c8c988b7a9af':
+        'community.wave.seqera.io/library/datavzrd:2.36.12--593eb75e566b7f2a' }"
+
+    input:
+    tuple val(meta), file(config_file), file(table)
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: report
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    datavzrd \\
+        ${args} \\
+        ${config_file} \\
+        --output ${prefix} \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        datavzrd: \$(echo \$( datavzrd --version | sed -e 's/[^0-9.]//g' ))
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    mkdir ${prefix}/static
+    mkdir ${prefix}/network
+    mkdir ${prefix}/network/data
+    mkdir ${prefix}/network/plots
+    touch ./${prefix}/index.html
+    touch ./${prefix}/static/bootstrap.min.css
+    touch ./${prefix}/static/bootstrap-select.min.css
+    touch ./${prefix}/static/bootstrap-table.min.css
+    touch ./${prefix}/static/bootstrap-table-fixed-columns.min.css
+    touch ./${prefix}/static/bundle.js
+    touch ./${prefix}/static/datavzrd.css
+    touch ./${prefix}/network/index_1.html
+    touch ./${prefix}/network/config.js
+    touch ./${prefix}/network/functions.js
+    touch ./${prefix}/network/heatmap.js
+    touch ./${prefix}/network/data/data_1.js
+    touch ./${prefix}/network/plots/plot_0.js
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        datavzrd: \$(echo \$( datavzrd --version | sed -e 's/[^0-9.]//g' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/datavzrd/meta.yml

@@ -0,0 +1,46 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "datavzrd"
+description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.
+keywords:
+  - visualisation
+  - tsv
+  - csv
+tools:
+  - datavzrd:
+      description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables.
+      homepage: https://datavzrd.github.io/
+      documentation: https://datavzrd.github.io/docs/index.html
+      tool_dev_url: https://github.com/datavzrd/datavzrd
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - config_file:
+      type: file
+      description: configuration file used for visualisation
+      pattern: "*.{yml,yaml}"
+  - table:
+      type: file
+      description: file used for visualisation
+      pattern: "*.{tsv,csv}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - report:
+      type: directory
+      description: directory with HTML report of provided CSV/TSV files
+      pattern: "/output/"
+
+authors:
+  - "@vickylaram"
+  - "@famosab"
+maintainers:
+  - "@famosab"

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

@@ -0,0 +1,112 @@
+nextflow_process {
+    name "Test Process DATAVZRD"
+    script "../main.nf"
+    process "DATAVZRD"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "datavzrd"
+
+    test("csv") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id: "csv_config"],
+                    file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                            process.out.versions,
+                            path(process.out.report[0][1])
+                                .list()
+                                .collect { getRecursiveFileNames(it, process.out.report[0][1]) }
+                                .flatten()
+                        ).match("csv")
+                    }
+            )
+        }
+    }
+
+    test("tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [ [id: "tsv_config"],
+                    file(params.modules_testdata_base_path + 'generic/config/config_network.datavzrd.yaml', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                            process.out.versions,
+                            path(process.out.report[0][1])
+                                .list()
+                                .collect { getRecursiveFileNames(it, process.out.report[0][1]) }
+                                .flatten()
+                        ).match("tsv")
+                    }
+            )
+        }
+    }
+
+    test("csv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [id: "csv_config"],
+                    file(params.modules_testdata_base_path + 'generic/config/config_test.datavzrd.yaml', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'generic/csv/test.csv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("no_config_file") {
+        when {
+            process {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.out['report'].isEmpty() },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
+
+def getRecursiveFileNames(fileOrDir, outputDir) {
+    if(file(fileOrDir.toString()).isDirectory()) {
+        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
+    }
+    return fileOrDir.toString().replace("${outputDir}/", "")
+}

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

@@ -0,0 +1,162 @@
+{
+    "csv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "csv_config"
+                        },
+                        [
+                            "index.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                "config.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                [
+                                    "data_1.js:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ],
+                                "functions.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "heatmap.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "index_1.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                [
+                                    "plot_0.js:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ],
+                            [
+                                "bootstrap-select.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap-table-fixed-columns.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap-table.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bundle.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "datavzrd.css:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ]
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "csv_config"
+                        },
+                        [
+                            "index.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            [
+                                "config.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                [
+                                    "data_1.js:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ],
+                                "functions.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "heatmap.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "index_1.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                [
+                                    "plot_0.js:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ],
+                            [
+                                "bootstrap-select.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap-table-fixed-columns.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap-table.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bootstrap.min.css:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "bundle.js:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "datavzrd.css:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ]
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-26T10:16:55.267548327"
+    },
+    "tsv": {
+        "content": [
+            [
+                "versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
+            ],
+            [
+                "index.html",
+                "network/config.js",
+                "network/data/data_1.js",
+                "network/functions.js",
+                "network/heatmap.js",
+                "network/index_1.html",
+                "network/plots/plot_0.js",
+                "network/plots/plot_1.js",
+                "network/plots/plot_2.js",
+                "network/plots/plot_3.js",
+                "static/bootstrap-select.min.css",
+                "static/bootstrap-table-fixed-columns.min.css",
+                "static/bootstrap-table.min.css",
+                "static/bootstrap.min.css",
+                "static/bundle.js",
+                "static/datavzrd.css"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-26T10:15:02.495557702"
+    },
+    "no_config_file": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "report": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-26T10:15:09.362847938"
+    },
+    "csv": {
+        "content": [
+            [
+                "versions.yml:md5,4c539593d78c0a07ede5759e0ce5ade8"
+            ],
+            [
+                "index.html",
+                "static/bootstrap-select.min.css",
+                "static/bootstrap-table-fixed-columns.min.css",
+                "static/bootstrap-table.min.css",
+                "static/bootstrap.min.css",
+                "static/bundle.js",
+                "static/datavzrd.css",
+                "test/config.js",
+                "test/data/data_1.js",
+                "test/functions.js",
+                "test/heatmap.js",
+                "test/index_1.html",
+                "test/plots/plot_0.js",
+                "test/plots/plot_1.js",
+                "test/plots/plot_2.js",
+                "test/plots/plot_3.js"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-26T10:14:58.495338891"
+    }
+}

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

@@ -0,0 +1,2 @@
+datavzrd:
+  - "modules/nf-core/datavzrd/**"