From b9672b553e9204ed4ea62b087aa00a01ca3f385f Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Thu, 2 May 2024 17:57:52 +1200
Subject: [PATCH] Added tirlearner

---
 .../tirlearner/environment.yml                |   9 +
 modules/edta-components/tirlearner/main.nf    |  64 ++++++
 modules/edta-components/tirlearner/meta.yml   |  64 ++++++
 .../tirlearner/tests/main.nf.test             |  68 +++++++
 .../tirlearner/tests/main.nf.test.snap        | 164 +++++++++++++++
 .../edta-components/tirlearner/tests/tags.yml |   2 +
 modules/environment-schema.json               |  34 ++++
 modules/meta-schema.json                      | 186 ++++++++++++++++++
 modules/nf-core/gunzip/environment.yml        |   7 +
 modules/nf-core/gunzip/main.nf                |  48 +++++
 modules/nf-core/gunzip/meta.yml               |  39 ++++
 modules/nf-core/gunzip/tests/main.nf.test     |  36 ++++
 .../nf-core/gunzip/tests/main.nf.test.snap    |  31 +++
 modules/nf-core/gunzip/tests/tags.yml         |   2 +
 modules/yaml-schema.json                      |   1 +
 nf-core-hybridisation.sh                      |   4 +
 nf-core-modules/.nf-core.yml                  |   1 +
 nf-core-modules/main.nf                       |   0
 nf-core-modules/modules.json                  |  17 ++
 .../modules/nf-core/gunzip/environment.yml    |   7 +
 .../modules/nf-core/gunzip/main.nf            |  48 +++++
 .../modules/nf-core/gunzip/meta.yml           |  39 ++++
 .../modules/nf-core/gunzip/tests/main.nf.test |  36 ++++
 .../nf-core/gunzip/tests/main.nf.test.snap    |  31 +++
 .../modules/nf-core/gunzip/tests/tags.yml     |   2 +
 nf-core-modules/nextflow.config               |   0
 tests/config/test_data.config                 |   2 +-
 27 files changed, 941 insertions(+), 1 deletion(-)
 create mode 100644 modules/edta-components/tirlearner/environment.yml
 create mode 100644 modules/edta-components/tirlearner/main.nf
 create mode 100644 modules/edta-components/tirlearner/meta.yml
 create mode 100644 modules/edta-components/tirlearner/tests/main.nf.test
 create mode 100644 modules/edta-components/tirlearner/tests/main.nf.test.snap
 create mode 100644 modules/edta-components/tirlearner/tests/tags.yml
 create mode 100644 modules/environment-schema.json
 create mode 100644 modules/meta-schema.json
 create mode 100644 modules/nf-core/gunzip/environment.yml
 create mode 100644 modules/nf-core/gunzip/main.nf
 create mode 100644 modules/nf-core/gunzip/meta.yml
 create mode 100644 modules/nf-core/gunzip/tests/main.nf.test
 create mode 100644 modules/nf-core/gunzip/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/gunzip/tests/tags.yml
 create mode 120000 modules/yaml-schema.json
 create mode 100644 nf-core-modules/.nf-core.yml
 create mode 100644 nf-core-modules/main.nf
 create mode 100644 nf-core-modules/modules.json
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/environment.yml
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/main.nf
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/meta.yml
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test.snap
 create mode 100644 nf-core-modules/modules/nf-core/gunzip/tests/tags.yml
 create mode 100644 nf-core-modules/nextflow.config

diff --git a/modules/edta-components/tirlearner/environment.yml b/modules/edta-components/tirlearner/environment.yml
new file mode 100644
index 0000000..36344b7
--- /dev/null
+++ b/modules/edta-components/tirlearner/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tirlearner"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::tir-learner=3.0.1"
diff --git a/modules/edta-components/tirlearner/main.nf b/modules/edta-components/tirlearner/main.nf
new file mode 100644
index 0000000..4da9520
--- /dev/null
+++ b/modules/edta-components/tirlearner/main.nf
@@ -0,0 +1,64 @@
+process TIRLEARNER {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tir-learner:3.0.1--hdfd78af_0':
+        'biocontainers/tir-learner:3.0.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    val species
+
+    output:
+    tuple val(meta), path("${prefix}.fa")           , emit: fasta
+    tuple val(meta), path("${prefix}.gff3")         , emit: gff
+    tuple val(meta), path("${prefix}.filtered.fa")  , emit: filtered_fasta
+    tuple val(meta), path("${prefix}.filtered.gff3"), emit: filtered_gff
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args     ?: ''
+    prefix      = task.ext.prefix   ?: "${meta.id}"
+    if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    TIR-Learner \\
+        -f $fasta \\
+        -s $species \\
+        -t $task.cpus \\
+        -o $prefix \\
+        $args
+
+    mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn.fa"           "${prefix}.fa"
+    mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn.gff3"         "${prefix}.gff3"
+
+    mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn_filter.fa"    "${prefix}.filtered.fa"
+    mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn_filter.gff3"  "${prefix}.filtered.gff3"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args    = task.ext.args ?: ''
+    prefix      = task.ext.prefix ?: "${meta.id}"
+    if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch "${prefix}.fa"
+    touch "${prefix}.gff3"
+
+    touch "${prefix}.filtered.fa"
+    touch "${prefix}.filtered.gff3"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/edta-components/tirlearner/meta.yml b/modules/edta-components/tirlearner/meta.yml
new file mode 100644
index 0000000..cb0af30
--- /dev/null
+++ b/modules/edta-components/tirlearner/meta.yml
@@ -0,0 +1,64 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "tirlearner"
+description: |
+  Ensemble Method for TIR Transposable Element Annotation
+keywords:
+  - genomics
+  - annotation
+  - repeat
+  - transposable
+tools:
+  - "TIR-Learner":
+      description: TIR-Learner
+      homepage: "https://github.com/lutianyu2001/TIR-Learner"
+      documentation: "https://github.com/lutianyu2001/TIR-Learner"
+      tool_dev_url: "https://github.com/lutianyu2001/TIR-Learner"
+      doi: "10.1016/j.molp.2019.02.008"
+      licence: ["GPLv3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fasta:
+      type: file
+      description: Genome sequences in fasta format
+      pattern: "*.{fsa,fa,fasta}"
+  - species:
+      type: string
+      description: |
+        "maize", "rice" or "others"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fasta:
+      type: file
+      description: Putative TIRs in fasta format
+      pattern: "*.fa"
+  - gff:
+      type: file
+      description: Putative TIRs in GFF3 format
+      pattern: "*.gff3"
+  - filtered_fasta:
+      type: file
+      description: Filtered TIRs in fasta format
+      pattern: "*.fa"
+  - filtered_gff:
+      type: file
+      description: Filtered TIRs in GFF3 format
+      pattern: "*.gff3"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@jguhlin"
+  - "@GallVp"
+maintainers:
+  - "@jguhlin"
+  - "@GallVp"
diff --git a/modules/edta-components/tirlearner/tests/main.nf.test b/modules/edta-components/tirlearner/tests/main.nf.test
new file mode 100644
index 0000000..0bb94d3
--- /dev/null
+++ b/modules/edta-components/tirlearner/tests/main.nf.test
@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process TIRLEARNER"
+    script "../main.nf"
+    process "TIRLEARNER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tirlearner"
+    tag "gunzip/main"
+
+    setup {
+        run('GUNZIP') {
+            script "../../../nf-core/gunzip/main"
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['actinidia_chinensis']['genome']['genome_1_fasta_gz'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("actinidia_chinensis-genome_1_fasta_gz-success") {
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = 'others'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = 'others'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/edta-components/tirlearner/tests/main.nf.test.snap b/modules/edta-components/tirlearner/tests/main.nf.test.snap
new file mode 100644
index 0000000..e245b2d
--- /dev/null
+++ b/modules/edta-components/tirlearner/tests/main.nf.test.snap
@@ -0,0 +1,164 @@
+{
+    "actinidia_chinensis-genome_1_fasta_gz-success": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,65987decb67d1e3f95b993f86d14c0d0"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,90bf040e7b29763351237207297dc801"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.fa:md5,65987decb67d1e3f95b993f86d14c0d0"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.gff3:md5,90bf040e7b29763351237207297dc801"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3d4a9683fc634e22fd79a4fbe0b23a30"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,65987decb67d1e3f95b993f86d14c0d0"
+                    ]
+                ],
+                "filtered_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.fa:md5,65987decb67d1e3f95b993f86d14c0d0"
+                    ]
+                ],
+                "filtered_gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.gff3:md5,90bf040e7b29763351237207297dc801"
+                    ]
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,90bf040e7b29763351237207297dc801"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3d4a9683fc634e22fd79a4fbe0b23a30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:35:56.356956"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,3d4a9683fc634e22fd79a4fbe0b23a30"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "filtered_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "filtered_gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3d4a9683fc634e22fd79a4fbe0b23a30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:36:08.718538"
+    }
+}
\ No newline at end of file
diff --git a/modules/edta-components/tirlearner/tests/tags.yml b/modules/edta-components/tirlearner/tests/tags.yml
new file mode 100644
index 0000000..190430a
--- /dev/null
+++ b/modules/edta-components/tirlearner/tests/tags.yml
@@ -0,0 +1,2 @@
+tirlearner:
+  - "modules/edta-components/tirlearner/**"
diff --git a/modules/environment-schema.json b/modules/environment-schema.json
new file mode 100644
index 0000000..ca7bdf6
--- /dev/null
+++ b/modules/environment-schema.json
@@ -0,0 +1,34 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "title": "conda environment yaml",
+    "description": "Validate the environment.yml file for an nf-core module",
+    "type": "object",
+    "properties": {
+        "name": {
+            "type": "string",
+            "description": "The name of the component, same as in the meta.yml"
+        },
+        "channels": {
+            "type": "array",
+            "items": [
+                {
+                    "enum": ["conda-forge"]
+                },
+                {
+                    "enum": ["bioconda"]
+                },
+                {
+                    "enum": ["defaults"]
+                }
+            ],
+            "minItems": 3
+        },
+        "dependencies": {
+            "type": "array",
+            "items": {
+                "type": "string"
+            }
+        }
+    },
+    "required": ["name", "channels", "dependencies"]
+}
diff --git a/modules/meta-schema.json b/modules/meta-schema.json
new file mode 100644
index 0000000..0b855d7
--- /dev/null
+++ b/modules/meta-schema.json
@@ -0,0 +1,186 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "title": "Meta yaml",
+    "description": "Validate the meta yaml file for an nf-core module",
+    "type": "object",
+    "properties": {
+        "name": {
+            "type": "string",
+            "description": "Name of the module"
+        },
+        "description": {
+            "type": "string",
+            "description": "Description of the module"
+        },
+        "keywords": {
+            "type": "array",
+            "description": "Keywords for the module",
+            "items": {
+                "type": "string"
+            },
+            "minItems": 3
+        },
+        "authors": {
+            "type": "array",
+            "description": "Authors of the module",
+            "items": {
+                "type": "string"
+            }
+        },
+        "maintainers": {
+            "type": "array",
+            "description": "Maintainers of the module",
+            "items": {
+                "type": "string"
+            }
+        },
+        "input": {
+            "type": "array",
+            "description": "Input channels for the module",
+            "items": {
+                "type": "object",
+                "patternProperties": {
+                    ".*": {
+                        "type": "object",
+                        "properties": {
+                            "type": {
+                                "type": "string",
+                                "description": "Type of the input channel",
+                                "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
+                            },
+                            "description": {
+                                "type": "string",
+                                "description": "Description of the input channel"
+                            },
+                            "pattern": {
+                                "type": "string",
+                                "description": "Pattern of the input channel, given in Java glob syntax"
+                            },
+                            "default": {
+                                "type": ["string", "number", "boolean", "array", "object"],
+                                "description": "Default value for the input channel"
+                            },
+                            "enum": {
+                                "type": "array",
+                                "description": "List of allowed values for the input channel",
+                                "items": {
+                                    "type": ["string", "number", "boolean", "array", "object"]
+                                },
+                                "uniqueItems": true
+                            }
+                        },
+                        "required": ["type", "description"]
+                    }
+                }
+            }
+        },
+        "output": {
+            "type": "array",
+            "description": "Output channels for the module",
+            "items": {
+                "type": "object",
+                "patternProperties": {
+                    ".*": {
+                        "type": "object",
+                        "properties": {
+                            "type": {
+                                "type": "string",
+                                "description": "Type of the output channel",
+                                "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
+                            },
+                            "description": {
+                                "type": "string",
+                                "description": "Description of the output channel"
+                            },
+                            "pattern": {
+                                "type": "string",
+                                "description": "Pattern of the input channel, given in Java glob syntax"
+                            },
+                            "enum": {
+                                "type": "array",
+                                "description": "List of allowed values for the output channel",
+                                "items": {
+                                    "type": ["string", "number", "boolean", "array", "object"]
+                                },
+                                "uniqueItems": true
+                            }
+                        },
+                        "required": ["type", "description"]
+                    }
+                }
+            }
+        },
+        "tools": {
+            "type": "array",
+            "description": "Tools used by the module",
+            "items": {
+                "type": "object",
+                "patternProperties": {
+                    ".*": {
+                        "type": "object",
+                        "properties": {
+                            "description": {
+                                "type": "string",
+                                "description": "Description of the output channel"
+                            },
+                            "homepage": {
+                                "type": "string",
+                                "description": "Homepage of the tool",
+                                "pattern": "^(http|https)://.*$"
+                            },
+                            "documentation": {
+                                "type": "string",
+                                "description": "Documentation of the tool",
+                                "pattern": "^(http|https|ftp)://.*$"
+                            },
+                            "tool_dev_url": {
+                                "type": "string",
+                                "description": "URL of the development version of the tool's documentation",
+                                "pattern": "^(http|https)://.*$"
+                            },
+                            "doi": {
+                                "description": "DOI of the tool",
+                                "anyOf": [
+                                    {
+                                        "type": "string",
+                                        "pattern": "^10\\.\\d{4,9}\\/[^,]+$"
+                                    },
+                                    {
+                                        "type": "string",
+                                        "enum": ["no DOI available"]
+                                    }
+                                ]
+                            },
+                            "licence": {
+                                "type": "array",
+                                "items": {
+                                    "type": "string"
+                                },
+                                "description": "Licence of the tool",
+                                "minItems": 1,
+                                "uniqueItems": true,
+                                "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
+                            }
+                        },
+                        "required": ["description"],
+                        "anyOf": [
+                            {
+                                "required": ["homepage"]
+                            },
+                            {
+                                "required": ["documentation"]
+                            },
+                            {
+                                "required": ["tool_dev_url"]
+                            },
+                            {
+                                "required": ["doi"]
+                            }
+                        ]
+                    }
+                }
+            }
+        }
+    },
+    "required": ["name", "description", "keywords", "authors", "output", "tools"]
+}
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
new file mode 100644
index 0000000..25910b3
--- /dev/null
+++ b/modules/nf-core/gunzip/environment.yml
@@ -0,0 +1,7 @@
+name: gunzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
new file mode 100644
index 0000000..468a6f2
--- /dev/null
+++ b/modules/nf-core/gunzip/main.nf
@@ -0,0 +1,48 @@
+process GUNZIP {
+    tag "$archive"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("$gunzip"), emit: gunzip
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    gunzip = archive.toString() - '.gz'
+    """
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
+        $args \\
+        $archive \\
+        > $gunzip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    gunzip = archive.toString() - '.gz'
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
new file mode 100644
index 0000000..231034f
--- /dev/null
+++ b/modules/nf-core/gunzip/meta.yml
@@ -0,0 +1,39 @@
+name: gunzip
+description: Compresses and decompresses files.
+keywords:
+  - gunzip
+  - compression
+  - decompression
+tools:
+  - gunzip:
+      description: |
+        gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Optional groovy Map containing meta information
+        e.g. [ id:'test', single_end:false ]
+  - archive:
+      type: file
+      description: File to be compressed/uncompressed
+      pattern: "*.*"
+output:
+  - gunzip:
+      type: file
+      description: Compressed/uncompressed file
+      pattern: "*.*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
new file mode 100644
index 0000000..6406008
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process GUNZIP"
+    script "../main.nf"
+    process "GUNZIP"
+    tag "gunzip"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
new file mode 100644
index 0000000..720fd9f
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-17T15:35:37.690477896"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml
new file mode 100644
index 0000000..fd3f691
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/tags.yml
@@ -0,0 +1,2 @@
+gunzip:
+  - modules/nf-core/gunzip/**
diff --git a/modules/yaml-schema.json b/modules/yaml-schema.json
new file mode 120000
index 0000000..d84030e
--- /dev/null
+++ b/modules/yaml-schema.json
@@ -0,0 +1 @@
+meta-schema.json
\ No newline at end of file
diff --git a/nf-core-hybridisation.sh b/nf-core-hybridisation.sh
index f1f641a..a92fb0c 100755
--- a/nf-core-hybridisation.sh
+++ b/nf-core-hybridisation.sh
@@ -1 +1,5 @@
 #!/usr/bin/env bash
+
+# Modules for tests
+mkdir -p ./modules/nf-core/gunzip
+cp -r ./nf-core-modules/modules/nf-core/gunzip/ ./modules/nf-core/gunzip/
diff --git a/nf-core-modules/.nf-core.yml b/nf-core-modules/.nf-core.yml
new file mode 100644
index 0000000..3805dc8
--- /dev/null
+++ b/nf-core-modules/.nf-core.yml
@@ -0,0 +1 @@
+repository_type: pipeline
diff --git a/nf-core-modules/main.nf b/nf-core-modules/main.nf
new file mode 100644
index 0000000..e69de29
diff --git a/nf-core-modules/modules.json b/nf-core-modules/modules.json
new file mode 100644
index 0000000..47010cc
--- /dev/null
+++ b/nf-core-modules/modules.json
@@ -0,0 +1,17 @@
+{
+    "name": "",
+    "homePage": "",
+    "repos": {
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/nf-core-modules/modules/nf-core/gunzip/environment.yml b/nf-core-modules/modules/nf-core/gunzip/environment.yml
new file mode 100644
index 0000000..25910b3
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/environment.yml
@@ -0,0 +1,7 @@
+name: gunzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/nf-core-modules/modules/nf-core/gunzip/main.nf b/nf-core-modules/modules/nf-core/gunzip/main.nf
new file mode 100644
index 0000000..468a6f2
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/main.nf
@@ -0,0 +1,48 @@
+process GUNZIP {
+    tag "$archive"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("$gunzip"), emit: gunzip
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    gunzip = archive.toString() - '.gz'
+    """
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
+        $args \\
+        $archive \\
+        > $gunzip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    gunzip = archive.toString() - '.gz'
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/nf-core-modules/modules/nf-core/gunzip/meta.yml b/nf-core-modules/modules/nf-core/gunzip/meta.yml
new file mode 100644
index 0000000..231034f
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/meta.yml
@@ -0,0 +1,39 @@
+name: gunzip
+description: Compresses and decompresses files.
+keywords:
+  - gunzip
+  - compression
+  - decompression
+tools:
+  - gunzip:
+      description: |
+        gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Optional groovy Map containing meta information
+        e.g. [ id:'test', single_end:false ]
+  - archive:
+      type: file
+      description: File to be compressed/uncompressed
+      pattern: "*.*"
+output:
+  - gunzip:
+      type: file
+      description: Compressed/uncompressed file
+      pattern: "*.*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test b/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test
new file mode 100644
index 0000000..6406008
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process GUNZIP"
+    script "../main.nf"
+    process "GUNZIP"
+    tag "gunzip"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test.snap b/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test.snap
new file mode 100644
index 0000000..720fd9f
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-17T15:35:37.690477896"
+    }
+}
\ No newline at end of file
diff --git a/nf-core-modules/modules/nf-core/gunzip/tests/tags.yml b/nf-core-modules/modules/nf-core/gunzip/tests/tags.yml
new file mode 100644
index 0000000..fd3f691
--- /dev/null
+++ b/nf-core-modules/modules/nf-core/gunzip/tests/tags.yml
@@ -0,0 +1,2 @@
+gunzip:
+  - modules/nf-core/gunzip/**
diff --git a/nf-core-modules/nextflow.config b/nf-core-modules/nextflow.config
new file mode 100644
index 0000000..e69de29
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 4633ce9..3c20520 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -661,7 +661,7 @@ params {
         }
         'actinidia_chinensis' {
             'genome' {
-                genome_21_fasta_gz              = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz"
+                genome_1_fasta_gz              = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz"
             }
         }
         'generic' {