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Add gcta/filtergrmwithkeep module
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‎modules/nf-core/gcta/filtergrmwithkeep/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::gcta=1.94.1

‎modules/nf-core/gcta/filtergrmwithkeep/main.nf‎

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process GCTA_FILTERGRMWITHKEEP {
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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 "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data'
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: 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
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input:
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tuple val(meta), path(grm_files)
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tuple val(meta2), path(keep_file)
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output:
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tuple val(meta), path("*_unrel.grm.*"), emit: filtered_grm
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tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: 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 extra_args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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gcta \\
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--grm ${meta.id} \\
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--keep ${keep_file} \\
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--make-grm \\
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--out ${prefix}_unrel \\
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--thread-num ${task.cpus} \\
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${extra_args}
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_unrel.grm.id
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touch ${prefix}_unrel.grm.bin
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touch ${prefix}_unrel.grm.N.bin
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"""
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}

‎modules/nf-core/gcta/filtergrmwithkeep/meta.yml‎

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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: "gcta_filtergrmwithkeep"
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description: Filter a dense GRM to the individuals listed in a keep file
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keywords:
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- gcta
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- genome-wide complex trait analysis
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- grm
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- genetic relationship matrix
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- genetics
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tools:
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- "gcta":
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description: "Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data."
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homepage: "https://yanglab.westlake.edu.cn/software/gcta/"
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documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf"
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tool_dev_url: "https://yanglab.westlake.edu.cn/software/gcta/"
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licence: ["GPL-3.0-only"]
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identifier: "biotools:gcta"
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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 dense GRM metadata
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e.g. `[ id:'plink_simulated' ]`
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`meta.id` is required and is the dense GRM basename contract used by `gcta --grm`.
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Input files must therefore be staged as `<meta.id>.grm.id`, `<meta.id>.grm.bin`, and `<meta.id>.grm.N.bin`.
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- grm_files:
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type: file
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description: Dense GRM file bundle
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pattern: "*.grm.*"
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ontologies: []
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- - meta2:
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type: map
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description: |
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Groovy map containing keep-file metadata
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e.g. `[ id:'plink_simulated_keep' ]`
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- keep_file:
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type: file
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description: Keep file listing the individuals to retain
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pattern: "*.{keep,txt,id}"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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output:
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filtered_grm:
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- - meta:
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type: map
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description: |
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Groovy map containing dense GRM metadata
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e.g. `[ id:'plink_simulated' ]`
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`meta.id` is preserved from the input dense GRM basename contract.
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- "*_unrel.grm.*":
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type: file
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description: Filtered GRM file bundle
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pattern: "*_unrel.grm.*"
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ontologies: []
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versions_gcta:
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- - "${task.process}":
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type: string
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description: The process the version was collected from
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- "gcta":
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type: string
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description: The tool name
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- "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
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type: eval
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description: The command used to retrieve the GCTA version
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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 process the version was collected from
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- gcta:
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type: string
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description: The tool name
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- "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'":
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type: eval
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description: The command used to retrieve the GCTA version
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authors:
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- "@lyh970817"
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maintainers:
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- "@lyh970817"

‎modules/nf-core/gcta/filtergrmwithkeep/tests/main.nf.test‎

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nextflow_process {
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name "Test Process GCTA_FILTERGRMWITHKEEP"
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script "../main.nf"
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process "GCTA_FILTERGRMWITHKEEP"
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tag "modules"
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tag "modules_nfcore"
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tag "gcta"
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tag "gcta/filtergrmwithkeep"
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tag "gcta/makegrm"
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tag "gcta/removerelatedsubjects"
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setup {
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run("GCTA_MAKEGRM", alias: "GCTA_MAKEGRM_DENSE") {
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script "../../makegrm/main.nf"
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process {
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"""
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file('plink_simulated.mpfile').text = 'plink_simulated plink_simulated.pgen plink_simulated.psam plink_simulated.pvar\\n'
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input[0] = [
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[ id:'plink_simulated_dense' ],
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file('plink_simulated.mpfile'),
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[
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true)
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],
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[
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true)
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],
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[
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', 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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run("GCTA_REMOVERELATEDSUBJECTS", alias: "GCTA_REMOVERELATEDSUBJECTS_KEEP") {
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script "../../removerelatedsubjects/main.nf"
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process {
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"""
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dense_grm = GCTA_MAKEGRM_DENSE.out.grm_files
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.map { meta, grm_files -> [[ id:meta.id ], grm_files] }
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input[0] = dense_grm
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"""
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}
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}
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}
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test("homo_sapiens popgen - filter dense GRM with keep file") {
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config "./nextflow.config"
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when {
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process {
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"""
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input[0] = GCTA_MAKEGRM_DENSE.out.grm_files.map { meta, grm_files -> [[ id:meta.id ], grm_files] }
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input[1] = GCTA_REMOVERELATEDSUBJECTS_KEEP.out.keep_file
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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 process.out.filtered_grm.size() == 1 },
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{ assert process.out.filtered_grm.get(0).get(0).id == "plink_simulated_dense" },
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{
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assert snapshot(
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process.out.filtered_grm
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).match("filtered_grm")
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},
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{
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def row = process.out.filtered_grm.get(0)
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assert row.get(1).every { file(it).exists() }
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assert row.get(1).collect { file(it).name }.sort() == [
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"plink_simulated_dense_unrel.grm.N.bin",
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"plink_simulated_dense_unrel.grm.bin",
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"plink_simulated_dense_unrel.grm.id"
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]
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},
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{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("versions") }
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)
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}
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}
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test("homo_sapiens popgen - fail when meta id does not match dense GRM basename") {
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config "./nextflow.config"
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when {
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process {
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"""
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input[0] = GCTA_MAKEGRM_DENSE.out.grm_files.map { meta, grm_files ->
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[[ id:'contract_dense_mismatch' ], grm_files]
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}
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input[1] = GCTA_REMOVERELATEDSUBJECTS_KEEP.out.keep_file
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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 process.exitStatus != 0 }
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)
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}
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}
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test("homo_sapiens popgen - filter dense GRM with keep file - stub") {
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options "-stub"
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config "./nextflow.config"
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when {
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process {
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"""
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input[0] = GCTA_MAKEGRM_DENSE.out.grm_files.map { meta, grm_files -> [[ id:meta.id ], grm_files] }
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input[1] = GCTA_REMOVERELATEDSUBJECTS_KEEP.out.keep_file
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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 process.out.filtered_grm.size() == 1 },
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{ assert process.out.filtered_grm.get(0).get(0).id == "plink_simulated_dense" },
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{
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assert snapshot(
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process.out.filtered_grm
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).match("stub_filtered_grm")
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},
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{
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def row = process.out.filtered_grm.get(0)
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assert row.get(1).every { file(it).exists() }
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assert row.get(1).collect { file(it).name }.sort() == [
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"plink_simulated_dense_unrel.grm.N.bin",
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"plink_simulated_dense_unrel.grm.bin",
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"plink_simulated_dense_unrel.grm.id"
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]
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},
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{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("stub_versions") }
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)
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}
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}
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}

‎modules/nf-core/gcta/filtergrmwithkeep/tests/main.nf.test.snap‎

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{
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"versions": {
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"content": [
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{
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"versions_gcta": [
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[
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"GCTA_FILTERGRMWITHKEEP",
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"gcta",
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"1.94.1"
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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": "2026-03-21T00:31:58.734112033"
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},
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"stub_filtered_grm": {
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"content": [
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[
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[
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{
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"id": "plink_simulated_dense"
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},
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[
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"plink_simulated_dense_unrel.grm.N.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
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"plink_simulated_dense_unrel.grm.bin:md5,d41d8cd98f00b204e9800998ecf8427e",
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"plink_simulated_dense_unrel.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e"
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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": "2026-05-15T23:16:45.31350454"
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},
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"filtered_grm": {
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"content": [
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[
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[
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{
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"id": "plink_simulated_dense"
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},
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[
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"plink_simulated_dense_unrel.grm.N.bin:md5,06b73ea8bae8f1e5f5d4de33dbd2c75e",
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"plink_simulated_dense_unrel.grm.bin:md5,b1f124463eecbae86840a6651eec372d",
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"plink_simulated_dense_unrel.grm.id:md5,ca8c0bded6951fdd3bf0dddc97b6df6b"
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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": "2026-05-15T23:14:49.332143185"
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},
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"stub_versions": {
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"content": [
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{
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"versions_gcta": [
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[
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"GCTA_FILTERGRMWITHKEEP",
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"gcta",
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"1.94.1"
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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": "2026-03-21T00:32:15.282563791"
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}
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}

‎modules/nf-core/gcta/filtergrmwithkeep/tests/nextflow.config‎

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params {
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modules_testdata_base_path = System.getenv("NF_MODULES_TESTDATA_BASE_PATH") ?: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
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}

‎modules/nf-core/gcta/makegrm/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::gcta=1.94.1

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