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Raw2ometiff (#8050)
* new modules raw2ometiff * update dependencies * test zarr dir * added singularity image * update input in meta.yml * nf-test with zarr.tar archive * update tag in nf.test * update test data dir * Update modules/nf-core/raw2ometiff/main.nf Co-authored-by: Famke Bäuerle <[email protected]> * Update modules/nf-core/raw2ometiff/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * update snapshot + test-dataset paths * update snapshot + nf-test assertions * update snapshot + review feedback --------- Co-authored-by: Famke Bäuerle <[email protected]>
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‎modules/nf-core/raw2ometiff/environment.yml

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- ome
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- conda-forge
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- bioconda
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dependencies:
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- "ome::raw2ometiff=0.7.1"
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- "conda-forge::blosc=1.21.6"

‎modules/nf-core/raw2ometiff/main.nf

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process RAW2OMETIFF {
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tag "$meta.id"
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label 'process_high'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/71/719a355f81f57ee91f5e3a66bb46687b81247eb55d84c2e57dce5d452f54b70a/data' :
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'community.wave.seqera.io/library/blosc_raw2ometiff:6ae5a6e69f313aa5'}"
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input:
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tuple val(meta), path(zarr_dir)
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output:
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tuple val(meta), path("*.ome.tiff"), emit: ometiff
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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raw2ometiff \\
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${zarr_dir} \\
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${prefix}.ome.tiff \\
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--max_workers $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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raw2ometiff: \$(raw2ometiff --version |& sed -n '1s/Version = //p')
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bio-formats: \$(bioformats2raw --version |& sed -n '2s/Bio-Formats version = //p')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.ome.tiff
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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raw2ometiff: \$(raw2ometiff --version |& sed -n '1s/Version = //p')
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bio-formats: \$(bioformats2raw --version |& sed -n '2s/Bio-Formats version = //p')
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END_VERSIONS
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"""
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}

‎modules/nf-core/raw2ometiff/meta.yml

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "raw2ometiff"
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description: write your description here
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keywords:
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- ome
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- tiff
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- imaging
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tools:
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- "raw2ometiff":
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description: "Java application to convert a directory of tiles to an OME-TIFF pyramid."
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homepage: "https://github.com/glencoesoftware/raw2ometiff"
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documentation: "https://github.com/glencoesoftware/raw2ometiff"
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tool_dev_url: "https://github.com/glencoesoftware/raw2ometiff"
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licence: ["GPL-2.0"]
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1']`
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- zarr_dir:
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type: directory
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description: Tile directory must contain a full pyramid in a Zarr container.
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pattern: "*.{zarr}"
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ontologies:
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- edam: "http://edamontology.org/format_3915"
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output:
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- ometiff:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1']`
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- "*.ome.tiff":
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type: file
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description: OME-TIFF pyramid
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pattern: "*.ome.tiff"
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ontologies:
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- edam: "http://edamontology.org/format_3727"
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- versions:
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- "versions.yml":
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@CaroAMN"
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maintainers:
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- "@CaroAMN"

‎modules/nf-core/raw2ometiff/tests/main.nf.test

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nextflow_process {
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name "Test Process RAW2OMETIFF"
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script "../main.nf"
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process "RAW2OMETIFF"
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tag "modules"
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tag "modules_nfcore"
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tag "raw2ometiff"
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tag "untar"
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test("raw2ometiff - zarr") {
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setup {
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run ("UNTAR") {
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script "../../untar/main.nf"
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process {
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"""
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input[0] = Channel.fromList([
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tuple([ id:'test'], // meta map
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file(params.modules_testdata_base_path + 'imaging/ome-zarr/zarr.tar', checkIfExists: true))
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])
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"""
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}
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}
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}
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when {
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process {
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"""
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input[0] = UNTAR.out.untar
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out.versions,
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file(process.out.ometiff[0][1]).name).match() }
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)
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}
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}
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test("raw2ometiff - zarr - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = Channel.fromList([
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tuple([ id:'test'], // meta map
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file(params.modules_testdata_base_path + 'imaging/ome-zarr/zarr.tar', checkIfExists: true))
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])
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

‎modules/nf-core/raw2ometiff/tests/main.nf.test.snap

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{
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"raw2ometiff - zarr - stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.ome.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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"versions.yml:md5,5b57fc6984255e5bde25ccdb231f8105"
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],
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"ometiff": [
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[
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{
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"id": "test"
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},
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"test.ome.tiff:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,5b57fc6984255e5bde25ccdb231f8105"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
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},
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"timestamp": "2025-06-16T11:18:15.608678597"
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},
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"raw2ometiff - zarr": {
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"content": [
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[
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"versions.yml:md5,5b57fc6984255e5bde25ccdb231f8105"
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],
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"test.ome.tiff"
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "24.10.4"
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},
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"timestamp": "2025-06-16T10:23:08.22317741"
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}
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}

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