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lbeltrameSPPearce
lbeltrame
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SPPearce
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Add finaletoolkit/endmotifs (#12035)
* Add finaletoolkit/endmotifs From the upstream documentation: > Measures frequency of k-mer 5’ end motifs. * Remove the export from the test, add it to the module * Update modules/nf-core/finaletoolkit/endmotifs/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/finaletoolkit/endmotifs/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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‎modules/nf-core/finaletoolkit/endmotifs/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::finaletoolkit=0.11.1"

‎modules/nf-core/finaletoolkit/endmotifs/main.nf‎

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process FINALETOOLKIT_ENDMOTIFS {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34f01d128ed135aedc33ddb62fced3911bef6d1a909694291b7184bf83719402/data'
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: 'community.wave.seqera.io/library/finaletoolkit:0.11.1--8fe5ba6ec9e2ec95'}"
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input:
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tuple val(meta), path(bam), path(bai)
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tuple val(meta2), path(genome)
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output:
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tuple val(meta), path("${prefix}.tsv"), emit: tsv
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tuple val("${task.process}"), val('finaletoolkit'), eval("finaletoolkit --version | sed 's/FinaleToolkit //g'"), topic: versions, emit: versions_finaletoolkit
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}_motifs"
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"""
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export MPLCONFIGDIR='./tmp'
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finaletoolkit \\
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end-motifs \\
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-w ${task.cpus} \\
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${bam} \\
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${genome} \\
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${args} \\
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-o "${prefix}.tsv"
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"""
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stub:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}_motifs"
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"""
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echo ${args}
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touch "${prefix}.tsv"
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"""
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}

‎modules/nf-core/finaletoolkit/endmotifs/meta.yml‎

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name: "finaletoolkit_endmotifs"
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description: |
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Measure the frequency of 5' k-mer end motifs.
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keywords:
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- end-motifs
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- genomics
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- fragmentomics
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tools:
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- "finaletoolkit":
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description: "Extract cfDNA fragmentation features from sequencing data."
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homepage: "https://epifluidlab.github.io/FinaleToolkit/"
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documentation: "https://epifluidlab.github.io/FinaleToolkit/documentation/index.html"
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tool_dev_url: "https://github.com/epifluidlab/FinaleToolkit"
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doi: "10.1093/bioadv/vbaf236"
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licence:
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- "MIT"
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identifier: biotools:finaletoolkit
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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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- bam:
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type: file
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description: Sorted BAM file
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pattern: "*.bam"
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ontologies:
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- edam: "http://edamontology.org/format_2572"
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- bai:
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type: file
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description: BAM file index
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pattern: "*.bai"
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ontologies:
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- edam: "http://edamontology.org/format_3327"
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- - meta2:
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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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- genome:
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type: file
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description: |
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FASTA or 2bit compressed genome file (must be the same as the one used for the
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BAM file)
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pattern: "*.2bit|*.fasta|*.fa"
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ontologies:
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- edam: "http://edamontology.org/format_3009"
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- edam: "http://edamontology.org/format_1929"
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output:
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tsv:
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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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- "${prefix}.tsv":
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type: file
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pattern: "*.tsv"
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description: |
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TSV file containing k-mer frequencies
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ontologies:
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- edam: "http://edamontology.org/format_3475"
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versions_finaletoolkit:
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- - ${task.process}:
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type: string
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description: The name of the process
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- finaletoolkit:
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type: string
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description: The name of the tool
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- finaletoolkit --version | sed 's/FinaleToolkit //g':
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- finaletoolkit:
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type: string
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description: The name of the tool
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- finaletoolkit --version | sed 's/FinaleToolkit //g':
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@lbeltrame"
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maintainers:
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- "@lbeltrame"

‎modules/nf-core/finaletoolkit/endmotifs/tests/main.nf.test‎

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nextflow_process {
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name "Test Process FINALETOOLKIT_ENDMOTIFS"
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script "../main.nf"
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process "FINALETOOLKIT_ENDMOTIFS"
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tag "modules"
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tag "modules_nfcore"
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tag "finaletoolkit"
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tag "finaletoolkit/endmotifs"
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test("homo_sapiens - bam") {
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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/homo_sapiens/illumina/bam/NA12878.chr22.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam.bai', checkIfExists: true),
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]
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input[1] = [
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[id: 'genome' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', 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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assert process.success
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assertAll(
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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test("homo_sapiens - 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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[],
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[]
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]
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input[1] = [
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[id: 'genome' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', 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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assert process.success
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assertAll(
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

‎modules/nf-core/finaletoolkit/endmotifs/tests/main.nf.test.snap‎

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{
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"homo_sapiens - stub": {
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"content": [
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{
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"tsv": [
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[
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{
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"id": "test"
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},
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"test_motifs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_finaletoolkit": [
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[
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"FINALETOOLKIT_ENDMOTIFS",
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"finaletoolkit",
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"0.11.1"
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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": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-06-18T10:03:20.535719738"
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},
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"homo_sapiens - bam": {
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"content": [
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{
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"tsv": [
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[
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{
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"id": "test"
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},
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"test_motifs.tsv:md5,bf6ce194a19bc80859a5b569b9075724"
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]
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],
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"versions_finaletoolkit": [
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[
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"FINALETOOLKIT_ENDMOTIFS",
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"finaletoolkit",
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"0.11.1"
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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": "0.9.3",
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"nextflow": "25.10.4"
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},
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"timestamp": "2026-06-18T09:58:04.501956285"
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}
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}

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