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mberacocheamberacochea
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Add the deacon/index tool. (#8640)
* Add the deacon/ / index tool. The container seems to have on apple sillicon, so I tested this locally using conda. * Adjust deacon/index based on PR feedback
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‎modules/nf-core/deacon/index/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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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::deacon=0.5.0"

‎modules/nf-core/deacon/index/main.nf

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process DEACON_INDEX {
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tag "$fasta"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deacon:0.5.0--h4349ce8_0':
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'biocontainers/deacon:0.5.0--h4349ce8_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.idx"), emit: index
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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deacon \\
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index \\
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build \\
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--threads ${task.cpus} \\
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$args \\
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$fasta > ${prefix}.idx
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${fasta.baseName}"
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"""
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touch ${prefix}.idx
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
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END_VERSIONS
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"""
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}

‎modules/nf-core/deacon/index/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: "deacon_index"
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description: Create deacon index for reference genome
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keywords:
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- index
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- fasta
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- genome
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- reference
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- minimizer
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- decontamination
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tools:
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- "deacon":
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description: "Fast alignment-free sequence filter"
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homepage: "https://github.com/bede/deacon"
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documentation: "https://github.com/bede/deacon#readme"
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tool_dev_url: "https://github.com/bede/deacon"
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doi: "10.1093/bioinformatics/btae004"
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licence: ["MIT"]
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identifier: "biotools:deacon"
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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 reference information.
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: Input genome fasta file
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pattern: "*.{fasta,fasta.gz,fas,fas.gz,fa,fa.gz,fna,fna.gz}"
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ontologies:
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- edam: "http://edamontology.org/data_2044" # Sequence
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- edam: "http://edamontology.org/format_1929" # FASTA
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output:
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- index:
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- meta:
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type: map
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description: |
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Groovy Map containing reference information.
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e.g. [ id:'test', single_end:false ]
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- "*.idx":
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type: file
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description: Deacon minimizer index file
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pattern: "*.idx"
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ontologies:
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- edam: "http://edamontology.org/data_3210" # Genome index
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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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- "@mberacochea"
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maintainers:
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- "@mberacochea"

‎modules/nf-core/deacon/index/tests/main.nf.test

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nextflow_process {
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name "Test Process DEACON_INDEX"
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script "../main.nf"
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process "DEACON_INDEX"
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tag "modules"
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tag "modules_nfcore"
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tag "deacon"
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tag "deacon/index"
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test("index sarscov2 - fasta") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test'],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', 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(
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process.out.index,
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process.out.versions.collect { path(it).yaml }
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).match()
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}
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)
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}
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}
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test("index sarscov2 - fasta gzipped") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test'],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', 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(
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process.out,
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process.out.versions.collect{ path(it).yaml }
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).match() }
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)
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}
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}
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test("index sarscov2 - fasta - 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] = [
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[ id:'test'],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', 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(
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process.out,
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process.out.versions.collect{ path(it).yaml }
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).match() }
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)
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}
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}
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}

‎modules/nf-core/deacon/index/tests/main.nf.test.snap

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{
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"index sarscov2 - fasta": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
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]
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],
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[
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{
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"DEACON_INDEX": {
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"deacon": "0.5.0"
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}
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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": "25.04.3"
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},
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"timestamp": "2025-06-16T08:54:38.622063"
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},
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"index sarscov2 - fasta - 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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"genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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"versions.yml:md5,60749febc4eaab16229dc078af00ea27"
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],
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"index": [
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[
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{
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"id": "test"
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},
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"genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,60749febc4eaab16229dc078af00ea27"
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]
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},
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[
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{
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"DEACON_INDEX": {
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"deacon": "0.5.0"
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}
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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": "25.04.3"
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},
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"timestamp": "2025-06-16T12:31:10.825365"
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},
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"index sarscov2 - fasta gzipped": {
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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.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
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]
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],
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"1": [
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"versions.yml:md5,60749febc4eaab16229dc078af00ea27"
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],
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"index": [
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[
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{
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"id": "test"
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},
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"test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
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]
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],
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"versions": [
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"versions.yml:md5,60749febc4eaab16229dc078af00ea27"
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]
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},
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[
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{
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"DEACON_INDEX": {
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"deacon": "0.5.0"
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}
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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": "25.04.3"
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},
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"timestamp": "2025-06-16T12:31:07.212408"
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}
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}

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