From b75874e11fe1e8636c9436e034ad9b2a82c86025 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 25 Nov 2024 17:06:16 +1300
Subject: [PATCH] Added mdust

---
 docs/AVAILABLE.txt                           |  1 +
 docs/index.html                              |  5 ++
 modules/gallvp/mdust/environment.yml         |  7 ++
 modules/gallvp/mdust/main.nf                 | 50 ++++++++++++++
 modules/gallvp/mdust/meta.yml                | 46 +++++++++++++
 modules/gallvp/mdust/tests/main.nf.test      | 56 ++++++++++++++++
 modules/gallvp/mdust/tests/main.nf.test.snap | 68 ++++++++++++++++++++
 7 files changed, 233 insertions(+)
 create mode 100644 modules/gallvp/mdust/environment.yml
 create mode 100644 modules/gallvp/mdust/main.nf
 create mode 100644 modules/gallvp/mdust/meta.yml
 create mode 100644 modules/gallvp/mdust/tests/main.nf.test
 create mode 100644 modules/gallvp/mdust/tests/main.nf.test.snap

diff --git a/docs/AVAILABLE.txt b/docs/AVAILABLE.txt
index b2fe100..5c0fa43 100644
--- a/docs/AVAILABLE.txt
+++ b/docs/AVAILABLE.txt
@@ -14,6 +14,7 @@
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/repeatmasker/repeatmasker">modules/gallvp/repeatmasker/repeatmasker</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/plotsr">modules/gallvp/plotsr</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/minimap2/align">modules/gallvp/minimap2/align</a></li>
+<li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/mdust">modules/gallvp/mdust</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrretriever/ltrretriever">modules/gallvp/ltrretriever/ltrretriever</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrretriever/lai">modules/gallvp/ltrretriever/lai</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrharvest">modules/gallvp/ltrharvest</a></li>
diff --git a/docs/index.html b/docs/index.html
index 788ccce..791a0b9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -170,6 +170,11 @@ <h1>gallvp/nxf-components</h1>
                     >modules/gallvp/minimap2/align</a
                 >
             </li>
+            <li>
+                <a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/mdust"
+                    >modules/gallvp/mdust</a
+                >
+            </li>
             <li>
                 <a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrretriever/ltrretriever"
                     >modules/gallvp/ltrretriever/ltrretriever</a
diff --git a/modules/gallvp/mdust/environment.yml b/modules/gallvp/mdust/environment.yml
new file mode 100644
index 0000000..df7809c
--- /dev/null
+++ b/modules/gallvp/mdust/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::mdust=2006.10.17"
diff --git a/modules/gallvp/mdust/main.nf b/modules/gallvp/mdust/main.nf
new file mode 100644
index 0000000..e68bb52
--- /dev/null
+++ b/modules/gallvp/mdust/main.nf
@@ -0,0 +1,50 @@
+process MDUST {
+    tag "$meta.id"
+    label 'process_single'
+
+    // WARN: Manually update when changing Bioconda assets
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mdust:2006.10.17--h470a237_1':
+        'biocontainers/mdust:2006.10.17--h470a237_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.fasta")    , emit: fasta
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets
+    if( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    mdust \\
+        $fasta \\
+        $args \\
+        > "${prefix}.fasta"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mdust: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets
+    if( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${prefix}.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mdust: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/gallvp/mdust/meta.yml b/modules/gallvp/mdust/meta.yml
new file mode 100644
index 0000000..3cb7c63
--- /dev/null
+++ b/modules/gallvp/mdust/meta.yml
@@ -0,0 +1,46 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "mdust"
+description: mdust from DFCI Gene Indices Software Tools
+keywords:
+  - genomics
+  - gene
+  - filter
+tools:
+  - "mdust":
+      description: ""
+      homepage: "https://github.com/lh3/mdust"
+      documentation: "https://github.com/lh3/mdust"
+      tool_dev_url: "https://github.com/lh3/mdust"
+      licence: ["The Artistic License"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Input fasta file
+        pattern: "*.{fa,fsa,faa,fas,fasta}"
+output:
+  - fasta:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.fasta":
+          type: file
+          description: Output fasta file
+          pattern: "*.fasta"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"
diff --git a/modules/gallvp/mdust/tests/main.nf.test b/modules/gallvp/mdust/tests/main.nf.test
new file mode 100644
index 0000000..f297c10
--- /dev/null
+++ b/modules/gallvp/mdust/tests/main.nf.test
@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process MDUST"
+    script "../main.nf"
+    process "MDUST"
+
+    tag "modules"
+    tag "modules_gallvp"
+    tag "mdust"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/gallvp/mdust/tests/main.nf.test.snap b/modules/gallvp/mdust/tests/main.nf.test.snap
new file mode 100644
index 0000000..bab999c
--- /dev/null
+++ b/modules/gallvp/mdust/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,049b6354208f3470a1713aa90aed5e6e"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,049b6354208f3470a1713aa90aed5e6e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-25T17:04:59.601616"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,049b6354208f3470a1713aa90aed5e6e"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,049b6354208f3470a1713aa90aed5e6e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-25T17:04:16.863703"
+    }
+}
\ No newline at end of file