Add rclone copy

modules/nf-core/rclone/copy/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:
+  - conda-forge::rclone=1.65.0

modules/nf-core/rclone/copy/main.nf

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+process RCLONE_COPY {
+
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data'
+        : 'community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be'}"
+
+    input:
+    tuple val(meta), val(source_path), val(destination_path)
+    path rclone_config
+
+    output:
+    tuple val(meta), path("rclone-copy.log"), emit: log
+    tuple val("${task.process}"), val('rclone'), eval("rclone --version | sed -n '1s/^rclone v//p'"), topic: versions, emit: versions_rclone
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def configArg = rclone_config ? "--config '${rclone_config}'" : ''
+    def transfers = task.cpus
+    def checkers = task.cpus
+
+    """
+    rclone ${configArg} copy ${args} \\
+        --log-file rclone-copy.log \\
+        --transfers ${transfers} \\
+        --checkers ${checkers} \\
+        "${source_path}" \\
+        "${destination_path}"
+    """
+
+    stub:
+    """
+    touch rclone-copy.log
+    """
+}

modules/nf-core/rclone/copy/meta.yml

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+name: "rclone_copy"
+description: Copy files or directories between local and/or remote storage using Rclone
+keywords:
+  - rclone
+  - copy
+  - sync
+  - data-transfer
+tools:
+  - "rclone":
+      description: "Rclone is a command line program to manage files on cloud storage"
+      homepage: "https://rclone.org/"
+      documentation: "https://rclone.org/docs/"
+      licence:
+        - "MIT"
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test', single_end:false ]
+    - source_path:
+        type: string
+        description: |
+          Source path to copy from. This should be a path understood by Rclone,
+          such as a local path or a configured remote path.
+          Examples: `data/input`, `s3:bucket/path`, `gs:bucket/path`,
+          `remote:path/to/data`.
+    - destination_path:
+        type: string
+        description: |
+          Destination path to copy to. This should be the fully resolved target
+          path understood by Rclone, such as a local path or a configured remote
+          path. The module does not append sample IDs, basenames, or modify this
+          path internally.
+          Examples: `results/output`, `s3:bucket/output`, `gs:bucket/output`,
+          `remote:path/to/output`.
+  - rclone_config:
+      type: file
+      description: |
+        Rclone configuration file defining the remotes used by source_path and/or
+        destination_path. Authentication and remote-specific options should be
+        configured in this file where possible.
+      pattern: "*.conf"
+      ontologies: []
+output:
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information.
+            e.g. [ id:'test', single_end:false ]
+      - rclone-copy.log:
+          type: file
+          description: Rclone log file generated during the copy operation.
+          pattern: "rclone-copy.log"
+          ontologies: []
+  versions_rclone:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - rclone:
+          type: string
+          description: The name of the tool
+      - rclone --version | sed -n '1s/^rclone v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - rclone:
+          type: string
+          description: The name of the tool
+      - rclone --version | sed -n '1s/^rclone v//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@antoniasaracco"
+maintainers:
+  - "@antoniasaracco"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be
+      build_id: bd-ff88b2e0040147be_1
+      scan_id: sc-ff88b2e0040147be_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be
+      build_id: bd-ff88b2e0040147be_1
+      scan_id: sc-ff88b2e0040147be_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be
+      build_id: bd-ff88b2e0040147be_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/rclone:1.65.0--ff88b2e0040147be
+      build_id: bd-ff88b2e0040147be_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c947c1a7171daf074310295417d0f0afe879275e1543fa5fc2a9711e7c2c72ab/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/rclone/copy/.conda-lock/linux_amd64-bd-ff88b2e0040147be_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/rclone/copy/.conda-lock/linux_arm64-bd-ff88b2e0040147be_1.txt

modules/nf-core/rclone/copy/tests/main.nf.test

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+nextflow_process {
+
+    name "Test RCLONE_COPY"
+    script "../main.nf"
+    process "RCLONE_COPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rclone"
+    tag "rclone/copy"
+
+    test("homo_sapiens - gvcf - copy from https - dry-run") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                def test_file_path = params.modules_testdata_base_path.replaceFirst(/^https?:\\/\\/[^\\/]+\\//, '') + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz'
+
+                input[0] = [
+                    [ id:'test' ],
+                    ':http:' + test_file_path,
+                    '/tmp/test.genome.vcf.gz'
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.log[0][1].endsWith("rclone-copy.log") },
+                { assert snapshot(process.out.versions_rclone).match("versions") }
+            )
+        }
+    }
+
+    test("homo_sapiens - gvcf - copy from https - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                def test_file_path = params.modules_testdata_base_path.replaceFirst(/^https?:\\/\\/[^\\/]+\\//, '') + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz'
+
+                input[0] = [
+                    [ id:'test' ],
+                    ':http:' + test_file_path,
+                    '/tmp/test.genome.vcf.gz'
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/rclone/copy/tests/main.nf.test.snap

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+{
+    "homo_sapiens - gvcf - copy from https - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "rclone-copy.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "RCLONE_COPY",
+                        "rclone",
+                        "1.65.0-DEV"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "rclone-copy.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_rclone": [
+                    [
+                        "RCLONE_COPY",
+                        "rclone",
+                        "1.65.0-DEV"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-09T15:32:10.498668888",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
+    },
+    "versions": {
+        "content": [
+            [
+                [
+                    "RCLONE_COPY",
+                    "rclone",
+                    "1.65.0-DEV"
+                ]
+            ]
+        ],
+        "timestamp": "2026-07-09T15:36:57.123442141",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
+    }
+}

modules/nf-core/rclone/copy/tests/nextflow.config

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+process {
+    withName: 'RCLONE_COPY' {
+        ext.args = {
+            def base_url = (params.modules_testdata_base_path =~ /^(https?:\/\/[^\/]+)/)[0][1]
+            "--dry-run --http-url '${base_url}' --no-check-certificate"
+        }
+    }
+}