Add rclone check and checksum

modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt

@@ -0,0 +1,81 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/conda-forge/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/rclone-1.74.3-h519d9b9_0.conda
+packages:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+build_number: 20
+sha256: 1dd3fffd892081df9726d7eb7e0dea6198962ba775bd88842135a4ddb4deb3c9
+md5: a9f577daf3de00bca7c3c76c0ecbd1de
+depends:
+- __glibc >=2.17,<3.0.a0
+- libgomp >=7.5.0
+constrains:
+- openmp_impl <0.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 28948
+timestamp: 1770939786096
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+sha256: 8e0a3b5e41272e5678499b5dfc4cddb673f9e935de01eb0767ce857001229f46
+md5: 57736f29cc2b0ec0b6c2952d3f101b6a
+depends:
+- __glibc >=2.17,<3.0.a0
+- _openmp_mutex >=4.5
+constrains:
+- libgcc-ng ==15.2.0=*_19
+- libgomp 15.2.0 he0feb66_19
+license: GPL-3.0-only WITH GCC-exception-3.1
+license_family: GPL
+size: 1041084
+timestamp: 1778269013026
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+sha256: 5abe4ab9d93f6c9757d654f1969ae2267d4505315c1f2f8fe705fd60af084f1b
+md5: faac990cb7aedc7f3a2224f2c9b0c26c
+depends:
+- __glibc >=2.17,<3.0.a0
+license: GPL-3.0-only WITH GCC-exception-3.1
+license_family: GPL
+size: 603817
+timestamp: 1778268942614
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+sha256: fc89f74bbe362fb29fa3c037697a89bec140b346a2469a90f7936d1d7ea4d8a3
+md5: fc21868a1a5aacc937e7a18747acb8a5
+depends:
+- __glibc >=2.17,<3.0.a0
+- libgcc >=14
+license: X11 AND BSD-3-Clause
+size: 918956
+timestamp: 1777422145199
+- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
+sha256: 4ce2e1ee31a6217998f78c31ce7dc0a3e0557d9238b51d49dd20c52d467a126d
+md5: f2c23a77b25efcad57d377b34bd84941
+depends:
+- __glibc >=2.17,<3.0.a0
+- libgcc >=14
+- ncurses >=6.5,<7.0a0
+license: GPL-2.0-or-later AND LGPL-2.0-or-later
+license_family: GPL
+size: 593603
+timestamp: 1769710381284
+- conda: https://conda.anaconda.org/conda-forge/linux-64/rclone-1.74.3-h519d9b9_0.conda
+sha256: 74a49ffb12e8c974519e856e5cb19d2a3c0aa9538847fa616149a4e7576a8106
+md5: df1b9c8554e9fdb3e7610cde037b0757
+license: MIT
+license_family: MIT
+size: 45039813
+timestamp: 1780709814295

modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt

@@ -0,0 +1,75 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/conda-forge/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-aarch64:
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rclone-1.74.3-h8f1e559_0.conda
+packages:
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda
+build_number: 20
+sha256: a2527b1d81792a0ccd2c05850960df119c2b6d8f5fdec97f2db7d25dc23b1068
+md5: 468fd3bb9e1f671d36c2cbc677e56f1d
+depends:
+- libgomp >=7.5.0
+constrains:
+- openmp_impl <0.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 28926
+timestamp: 1770939656741
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_19.conda
+sha256: 4592b096e553f67799ae70d4b6167eeda3ec74587d68c7aecbf4e7b1df136681
+md5: f35b3f52d0a2ec4ffe3c89ba135cdb9a
+depends:
+- _openmp_mutex >=4.5
+constrains:
+- libgomp 15.2.0 h8acb6b2_19
+- libgcc-ng ==15.2.0=*_19
+license: GPL-3.0-only WITH GCC-exception-3.1
+license_family: GPL
+size: 622462
+timestamp: 1778268755949
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_19.conda
+sha256: 2370ef0ffcbae5bede3c4bf136add4abc257245eb91f724c99bb4a43116c5a83
+md5: c5e8a379c4a2ec2aea4ba22758c001d9
+license: GPL-3.0-only WITH GCC-exception-3.1
+license_family: GPL
+size: 587387
+timestamp: 1778268674393
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.6-hf8d1292_0.conda
+sha256: 369db85c5cd8d99dde364ce70725d76511d9c8199e5b820c740414091bf5bcca
+md5: b2a43456aa56fe80c2477a5094899eff
+depends:
+- libgcc >=14
+license: X11 AND BSD-3-Clause
+size: 960036
+timestamp: 1777422174534
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
+sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402
+md5: ab7288cc39545556d1bc5e71ab2df9a9
+depends:
+- libgcc >=14
+- ncurses >=6.5,<7.0a0
+license: GPL-2.0-or-later AND LGPL-2.0-or-later
+license_family: GPL
+size: 636733
+timestamp: 1769712412683
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rclone-1.74.3-h8f1e559_0.conda
+sha256: 6aef9a68af8b200db69a915073ba2285e01e95e363626921497074588fbd8493
+md5: d63c4d8337e3a0128716f6f515a1ed05
+license: MIT
+license_family: MIT
+size: 41497679
+timestamp: 1780709811705

modules/nf-core/rclone/check/environment.yml

@@ -0,0 +1,6 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+dependencies:
+  - "conda-forge::rclone=1.74.3"

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

@@ -0,0 +1,57 @@
+process RCLONE_CHECK {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+            ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data'
+            : 'community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97' }"
+
+    input:
+    tuple val(meta), path(source, stageAs: 'source/*')
+    tuple val(meta2), path(destination, stageAs: 'destination/*')
+
+    output:
+    tuple val(meta), path("${prefix}.combined.txt")       , emit: combined      , optional: true
+    tuple val(meta), path("${prefix}.differ.txt")         , emit: differ        , optional: true
+    tuple val(meta), path("${prefix}.missing_on_dst.txt") , emit: missing_on_dst, optional: true
+    tuple val(meta), path("${prefix}.missing_on_src.txt") , emit: missing_on_src, optional: true
+    tuple val(meta), path("${prefix}.match.txt")          , emit: match         , optional: true
+    tuple val(meta), path("${prefix}.error.txt")          , emit: error         , optional: true
+    tuple val("${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 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    rclone check \\
+        --copy-links \\
+        $args \\
+        --combined ${prefix}.combined.txt \\
+        --differ ${prefix}.differ.txt \\
+        --missing-on-dst ${prefix}.missing_on_dst.txt \\
+        --missing-on-src ${prefix}.missing_on_src.txt \\
+        --match ${prefix}.match.txt \\
+        --error ${prefix}.error.txt \\
+        --checkers $task.cpus \\
+        source \\
+        destination || true
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch \\
+        ${prefix}.combined.txt \\
+        ${prefix}.differ.txt \\
+        ${prefix}.missing_on_dst.txt \\
+        ${prefix}.missing_on_src.txt \\
+        ${prefix}.match.txt \\
+        ${prefix}.error.txt
+    """
+}

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

@@ -0,0 +1,161 @@
+name: "rclone_check"
+description: Check that files in source and destination paths match
+keywords:
+  - check
+  - checksum
+  - cloud
+  - sync
+tools:
+  - "rclone":
+      description: "Rclone is a command-line program to manage files on cloud storage."
+      homepage: "https://rclone.org/"
+      documentation: "https://rclone.org/commands/rclone_check/"
+      tool_dev_url: "https://github.com/rclone/rclone"
+      licence:
+        - "MIT"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing source information
+          e.g. [ id:'test' ]
+    - source:
+        type: file
+        description: File or directory containing source files to compare.
+        pattern: ""
+        ontologies:
+          - edam: "http://edamontology.org/data_0006"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing destination information
+          e.g. [ id:'test_dst' ]
+    - destination:
+        type: file
+        description: File or directory containing destination files to compare.
+        pattern: ""
+        ontologies:
+          - edam: "http://edamontology.org/data_0006"
+output:
+  combined:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.combined.txt:
+          type: file
+          description: Combined report of matching, missing, differing, and error paths.
+          pattern: "*.combined.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  differ:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.differ.txt:
+          type: file
+          description: Report of paths present in both source and destination but different.
+          pattern: "*.differ.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  missing_on_dst:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.missing_on_dst.txt:
+          type: file
+          description: Report of paths present in source but missing from destination.
+          pattern: "*.missing_on_dst.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  missing_on_src:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.missing_on_src.txt:
+          type: file
+          description: Report of paths present in destination but missing from source.
+          pattern: "*.missing_on_src.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  match:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.match.txt:
+          type: file
+          description: Report of matching paths.
+          pattern: "*.match.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  error:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing source information
+            e.g. [ id:'test' ]
+      - ${prefix}.error.txt:
+          type: file
+          description: Report of paths with read or hash errors.
+          pattern: "*.error.txt"
+          ontologies:
+            - edam: "http://edamontology.org/data_3671"
+  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:
+  - "@atrigila"
+maintainers:
+  - "@atrigila"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/rclone:1.74.3--351f8e39202b129a
+      build_id: bd-351f8e39202b129a_1
+      scan_id: sc-0e6358c70409ff39_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/rclone:1.74.3--2ef33c5b9132aa97
+      build_id: bd-2ef33c5b9132aa97_1
+      scan_id: sc-2cbce8a89ac463aa_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/rclone:1.74.3--af6486c6ac506f82
+      build_id: bd-af6486c6ac506f82_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5d/5dfd28fd0090c69f57c9bd93ea3235d8df194e8f269b5cb3027b6b59bff567d5/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/rclone:1.74.3--49a53709aa05d28d
+      build_id: bd-49a53709aa05d28d_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de06d232599f015aa253f63b84ba2e257bb542810dc11714b88ca9b4045b80ea/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/rclone/check/.conda-lock/linux_amd64-bd-2ef33c5b9132aa97_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/rclone/check/.conda-lock/linux_arm64-bd-351f8e39202b129a_1.txt