diff --git a/modules/nf-core/gcta/makegrm/environment.yml b/modules/nf-core/gcta/makegrm/environment.yml new file mode 100644 index 00000000000..3e22ea7b9f2 --- /dev/null +++ b/modules/nf-core/gcta/makegrm/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gcta=1.94.1 diff --git a/modules/nf-core/gcta/makegrm/main.nf b/modules/nf-core/gcta/makegrm/main.nf new file mode 100644 index 00000000000..0bb78639e36 --- /dev/null +++ b/modules/nf-core/gcta/makegrm/main.nf @@ -0,0 +1,42 @@ +process GCTA_MAKEGRM { + tag "${meta.id}" + label 'process_medium' + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data' + : 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}" + + input: + tuple val(meta), path(mfile), path(bed_pgen), path(bim_pvar), path(fam_psam) + + output: + tuple val(meta), path("*.grm.*"), emit: grm_files + tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + def extra_args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def genotype_files = bed_pgen instanceof List ? bed_pgen : [bed_pgen] + def genotype_extension = genotype_files[0].name.tokenize('.').last() + def multi_file_flag = genotype_extension == 'pgen' ? '--mpfile' : '--mbfile' + + """ + + gcta \\ + ${multi_file_flag} ${mfile} \\ + --make-grm \\ + --thread-num ${task.cpus} \\ + --out ${prefix} ${extra_args} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.grm.id + touch ${prefix}.grm.bin + touch ${prefix}.grm.N.bin + """ +} diff --git a/modules/nf-core/gcta/makegrm/meta.yml b/modules/nf-core/gcta/makegrm/meta.yml new file mode 100644 index 00000000000..0c813dadada --- /dev/null +++ b/modules/nf-core/gcta/makegrm/meta.yml @@ -0,0 +1,91 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "gcta_makegrm" +description: Compute a whole dense GRM with GCTA +keywords: + - gcta + - genome-wide complex trait analysis + - grm + - genetic relationship matrix + - genetics +tools: + - "gcta": + description: "GCTA is a tool for genome-wide complex trait analysis." + homepage: "https://yanglab.westlake.edu.cn/software/gcta/" + documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf" + tool_dev_url: "https://github.com/jianyangqt/gcta" + licence: + - "GPL-3.0-only" + identifier: biotools:gcta + +input: + - - meta: + type: map + description: | + Groovy Map containing GRM sample metadata + e.g. `[ id:'gcta_grm' ]` + - mfile: + type: file + description: GCTA multi-input manifest consumed by `--mbfile` or + `--mpfile` + pattern: "*.{mbfile,mpfile,txt}" + ontologies: + - edam: "http://edamontology.org/format_2330" + - bed_pgen: + type: file + description: Collection of PLINK primary genotype files referenced by the + multi-input manifest + pattern: "*.{bed,pgen}" + ontologies: + - edam: "http://edamontology.org/format_3003" + - bim_pvar: + type: file + description: Collection of PLINK variant metadata files referenced by the + multi-input manifest + pattern: "*.{bim,pvar}" + ontologies: [] + - fam_psam: + type: file + description: Collection of PLINK sample metadata files referenced by the + multi-input manifest + pattern: "*.{fam,psam}" + ontologies: [] + +output: + grm_files: + - - meta: + type: map + description: | + Groovy Map containing GRM sample metadata + e.g. `[ id:'gcta_grm' ]` + - "*.grm.*": + type: file + description: Dense GRM sidecar files + pattern: "*.grm.{id,bin,N.bin}" + ontologies: [] + versions_gcta: + - - ${task.process}: + type: string + description: The process the version was collected from + - gcta: + type: string + description: The tool name + - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": + type: eval + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - gcta: + type: string + description: The tool name + - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": + type: eval + description: The command used to generate the version of the tool + +authors: + - "@lyh970817" +maintainers: + - "@lyh970817" diff --git a/modules/nf-core/gcta/makegrm/tests/main.nf.test b/modules/nf-core/gcta/makegrm/tests/main.nf.test new file mode 100644 index 00000000000..e5c63233678 --- /dev/null +++ b/modules/nf-core/gcta/makegrm/tests/main.nf.test @@ -0,0 +1,142 @@ +nextflow_process { + + name "Test Process GCTA_MAKEGRM" + script "../main.nf" + process "GCTA_MAKEGRM" + + tag "modules" + tag "modules_nfcore" + tag "gcta" + tag "gcta/makegrm" + + test("homo_sapiens popgen - plink2") { + when { + process { + """ + file('gcta_grm.mpfile').text = 'plink_simulated plink_simulated.pgen plink_simulated.psam plink_simulated.pvar\\n' + + input[0] = [ + [ id:'gcta_grm' ], + file('gcta_grm.mpfile'), + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.grm_files.size() == 1 }, + { assert process.out.grm_files.get(0).get(0).id == 'gcta_grm' }, + { assert process.out.grm_files.get(0).get(0).keySet() == ['id'] as Set }, + { assert process.out.grm_files.get(0).get(1).size() == 3 }, + { + assert process.out.grm_files.get(0).get(1).collect { file(it).name }.toSet() == [ + 'gcta_grm.grm.id', + 'gcta_grm.grm.bin', + 'gcta_grm.grm.N.bin' + ] as Set + }, + { assert file(path(process.out.grm_files.get(0).get(1)[0]).parent.toString() + '/.command.sh').text.contains('--make-grm') }, + { assert file(path(process.out.grm_files.get(0).get(1)[0]).parent.toString() + '/.command.sh').text.contains('--mpfile') }, + { + assert snapshot( + process.out.grm_files, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() + } + ) + } + } + + test("homo_sapiens popgen - plink1") { + when { + process { + """ + file('gcta_grm.mbfile').text = 'plink_simulated\\n' + + input[0] = [ + [ id:'gcta_grm_bed' ], + file('gcta_grm.mbfile'), + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.grm_files.size() == 1 }, + { assert process.out.grm_files.get(0).get(0).id == 'gcta_grm_bed' }, + { assert process.out.grm_files.get(0).get(0).keySet() == ['id'] as Set }, + { assert process.out.grm_files.get(0).get(1).size() == 3 }, + { + assert process.out.grm_files.get(0).get(1).collect { file(it).name }.toSet() == [ + 'gcta_grm_bed.grm.id', + 'gcta_grm_bed.grm.bin', + 'gcta_grm_bed.grm.N.bin' + ] as Set + }, + { assert file(path(process.out.grm_files.get(0).get(1)[0]).parent.toString() + '/.command.sh').text.contains('--make-grm') }, + { assert file(path(process.out.grm_files.get(0).get(1)[0]).parent.toString() + '/.command.sh').text.contains('--mbfile') }, + { + assert snapshot( + process.out.grm_files, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() + } + ) + } + } + + test("homo_sapiens popgen - plink1 - stub") { + options "-stub" + + when { + process { + """ + file('gcta_grm.mbfile').text = 'plink_simulated\\n' + + input[0] = [ + [ id:'gcta_grm_bed' ], + file('gcta_grm.mbfile'), + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/gcta/makegrm/tests/main.nf.test.snap b/modules/nf-core/gcta/makegrm/tests/main.nf.test.snap new file mode 100644 index 00000000000..f8fbe133d5a --- /dev/null +++ b/modules/nf-core/gcta/makegrm/tests/main.nf.test.snap @@ -0,0 +1,111 @@ +{ + "homo_sapiens popgen - plink2": { + "content": [ + [ + [ + { + "id": "gcta_grm" + }, + [ + "gcta_grm.grm.N.bin:md5,acaa43bbbf2253d392537a178ecf09a4", + "gcta_grm.grm.bin:md5,45f8dff14bda17d50009a21050572228", + "gcta_grm.grm.id:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + { + "versions_gcta": [ + [ + "GCTA_MAKEGRM", + "gcta", + "1.94.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-15T21:08:43.209734458" + }, + "homo_sapiens popgen - plink1": { + "content": [ + [ + [ + { + "id": "gcta_grm_bed" + }, + [ + "gcta_grm_bed.grm.N.bin:md5,acaa43bbbf2253d392537a178ecf09a4", + "gcta_grm_bed.grm.bin:md5,45f8dff14bda17d50009a21050572228", + "gcta_grm_bed.grm.id:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + { + "versions_gcta": [ + [ + "GCTA_MAKEGRM", + "gcta", + "1.94.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-15T21:09:34.058651287" + }, + "homo_sapiens popgen - plink1 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "gcta_grm_bed" + }, + [ + "gcta_grm_bed.grm.N.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "gcta_grm_bed.grm.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "gcta_grm_bed.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "GCTA_MAKEGRM", + "gcta", + "1.94.1" + ] + ], + "grm_files": [ + [ + { + "id": "gcta_grm_bed" + }, + [ + "gcta_grm_bed.grm.N.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "gcta_grm_bed.grm.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "gcta_grm_bed.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_gcta": [ + [ + "GCTA_MAKEGRM", + "gcta", + "1.94.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-15T21:10:21.024687128" + } +} \ No newline at end of file diff --git a/modules/nf-core/gcta/makegrm/tests/nextflow.config b/modules/nf-core/gcta/makegrm/tests/nextflow.config new file mode 100644 index 00000000000..de31e021882 --- /dev/null +++ b/modules/nf-core/gcta/makegrm/tests/nextflow.config @@ -0,0 +1,3 @@ +params { + modules_testdata_base_path = System.getenv("NF_MODULES_TESTDATA_BASE_PATH") ?: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" +} diff --git a/modules/nf-core/gcta/removerelatedsubjects/environment.yml b/modules/nf-core/gcta/removerelatedsubjects/environment.yml new file mode 100644 index 00000000000..3e22ea7b9f2 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gcta=1.94.1 diff --git a/modules/nf-core/gcta/removerelatedsubjects/main.nf b/modules/nf-core/gcta/removerelatedsubjects/main.nf new file mode 100644 index 00000000000..539e2cf4ae6 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/main.nf @@ -0,0 +1,42 @@ +process GCTA_REMOVERELATEDSUBJECTS { + tag "${meta.id}" + label 'process_medium' + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data' + : 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}" + + input: + tuple val(meta), path(grm_files) + + output: + tuple val(meta), path("*_unrel05.grm.*"), emit: grm_files + tuple val(meta), path("*_unrel05.grm.id"), emit: keep_file + tuple val("${task.process}"), val("gcta"), eval("gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'"), emit: versions_gcta, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + def extra_args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + + gcta \\ + --grm ${meta.id} \\ + --grm-cutoff 0.05 \\ + --make-grm \\ + --out ${prefix}_unrel05 \\ + --thread-num ${task.cpus} \\ + ${extra_args} + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_unrel05.grm.id + touch ${prefix}_unrel05.grm.bin + touch ${prefix}_unrel05.grm.N.bin + """ +} diff --git a/modules/nf-core/gcta/removerelatedsubjects/meta.yml b/modules/nf-core/gcta/removerelatedsubjects/meta.yml new file mode 100644 index 00000000000..17b4ff7f298 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/meta.yml @@ -0,0 +1,83 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "gcta_removerelatedsubjects" +description: Remove related individuals from a dense GRM using `gcta --grm-cutoff` +keywords: + - gcta + - genome-wide complex trait analysis + - grm + - genetic relationship matrix + - genetics +tools: + - "gcta": + description: "Genome-wide Complex Trait Analysis (GCTA) estimates genetic relationships, variance components, and association statistics from genome-wide data." + homepage: "https://yanglab.westlake.edu.cn/software/gcta/" + documentation: "https://yanglab.westlake.edu.cn/software/gcta/static/gcta_doc_latest.pdf" + tool_dev_url: "https://yanglab.westlake.edu.cn/software/gcta/" + licence: ["GPL-3.0-only"] + identifier: "biotools:gcta" + +input: + - - meta: + type: map + description: | + Groovy map containing dense GRM metadata. + `meta.id` is the required GRM basename consumed by `--grm` and must match + the staged dense GRM files. + e.g. `[ id:'tiny_dense' ]` requires + `tiny_dense.grm.id`, `tiny_dense.grm.bin`, and `tiny_dense.grm.N.bin`. + - grm_files: + type: file + description: Dense GRM file bundle with basename `${meta.id}` + pattern: "*.grm.*" + ontologies: [] + +output: + grm_files: + - - meta: + type: map + description: | + Groovy map containing dense GRM metadata. + `meta.id` remains the dense-GRM basename contract used for `--grm`. + - "*_unrel05.grm.*": + type: file + description: Relatedness-filtered GRM file bundle + pattern: "*_unrel05.grm.*" + ontologies: [] + keep_file: + - - meta: + type: map + description: | + Groovy map containing dense GRM metadata. + `meta.id` remains the dense-GRM basename contract used for `--grm`. + - "*_unrel05.grm.id": + type: file + description: Keep file of unrelated individuals emitted by GCTA + pattern: "*_unrel05.grm.id" + ontologies: [] + versions_gcta: + - - "${task.process}": + type: string + description: The process the version was collected from + - "gcta": + type: string + description: The tool name + - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": + type: eval + description: The command used to retrieve the GCTA version + +topics: + versions: + - - ${task.process}: + type: string + description: The process the version was collected from + - gcta: + type: string + description: The tool name + - "gcta --version | sed -En 's/^[*] version v([0-9.]*).*/\\1/p'": + type: eval + description: The command used to retrieve the GCTA version + +authors: + - "@lyh970817" +maintainers: + - "@lyh970817" diff --git a/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test b/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test new file mode 100644 index 00000000000..722026e4c98 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test @@ -0,0 +1,174 @@ +nextflow_process { + + name "Test Process GCTA_REMOVERELATEDSUBJECTS" + script "../main.nf" + process "GCTA_REMOVERELATEDSUBJECTS" + + tag "modules" + tag "modules_nfcore" + tag "gcta" + tag "gcta/removerelatedsubjects" + tag "gcta/makegrm" + + setup { + run("GCTA_MAKEGRM", alias: "GCTA_MAKEGRM_CONTRACT") { + script "../../makegrm/main.nf" + process { + """ + file('tiny_dense.mbfile').text = 'plink_simulated\\n' + + input[0] = [ + [ id:'tiny_dense' ], + file('tiny_dense.mbfile'), + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true) + ] + ] + """ + } + } + + run("GCTA_MAKEGRM", alias: "GCTA_MAKEGRM_STUB") { + script "../../makegrm/main.nf" + process { + """ + file('stub_dense.mbfile').text = 'plink_simulated\\n' + + input[0] = [ + [ id:'stub_dense' ], + file('stub_dense.mbfile'), + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true) + ] + ] + """ + } + } + } + + test("homo_sapiens popgen - remove related individuals from dense GRM") { + config "./nextflow.config" + + when { + process { + """ + input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.grm_files.size() == 1 }, + { assert process.out.keep_file.size() == 1 }, + { assert process.out.grm_files.get(0).get(0).id == "tiny_dense" }, + { + def grm_row = process.out.grm_files.get(0) + def expected_prefix = "${grm_row.get(0).id}_unrel05" + assert grm_row.get(1).collect { file(it).name }.sort() == [ + "${expected_prefix}.grm.N.bin", + "${expected_prefix}.grm.bin", + "${expected_prefix}.grm.id" + ] + assert file(process.out.keep_file.get(0).get(1)).name == "${expected_prefix}.grm.id" + }, + { + assert snapshot( + process.out.grm_files, + process.out.keep_file, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() + } + ) + } + } + + test("homo_sapiens popgen - remove related individuals fails when meta.id is not GRM basename") { + config "./nextflow.config" + + when { + process { + """ + input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files.map { meta, grm_files -> + [[ id:'tiny_dense_mismatched' ], grm_files] + } + """ + } + } + + then { + assertAll( + { assert !process.success }, + { assert process.exitStatus != 0 } + ) + } + } + + test("homo_sapiens popgen - remove related individuals fails for malformed GRM tuple") { + config "./nextflow.config" + + when { + process { + """ + input[0] = GCTA_MAKEGRM_CONTRACT.out.grm_files.map { meta, grm_files -> + [[ id:meta.id ]] + } + """ + } + } + + then { + assert !process.success + } + } + + test("homo_sapiens popgen - remove related individuals from dense GRM - stub") { + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = GCTA_MAKEGRM_STUB.out.grm_files + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.grm_files.get(0).get(0).id == "stub_dense" }, + { + def grm_row = process.out.grm_files.get(0) + def expected_prefix = "${grm_row.get(0).id}_unrel05" + assert grm_row.get(1).collect { file(it).name }.sort() == [ + "${expected_prefix}.grm.N.bin", + "${expected_prefix}.grm.bin", + "${expected_prefix}.grm.id" + ] + assert file(process.out.keep_file.get(0).get(1)).name == "${expected_prefix}.grm.id" + }, + { + assert snapshot( + process.out.grm_files, + process.out.keep_file, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test.snap b/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test.snap new file mode 100644 index 00000000000..1c3d480ba73 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "homo_sapiens popgen - remove related individuals from dense GRM": { + "content": [ + [ + [ + { + "id": "tiny_dense" + }, + [ + "tiny_dense_unrel05.grm.N.bin:md5,06b73ea8bae8f1e5f5d4de33dbd2c75e", + "tiny_dense_unrel05.grm.bin:md5,b1f124463eecbae86840a6651eec372d", + "tiny_dense_unrel05.grm.id:md5,ca8c0bded6951fdd3bf0dddc97b6df6b" + ] + ] + ], + [ + [ + { + "id": "tiny_dense" + }, + "tiny_dense_unrel05.grm.id:md5,ca8c0bded6951fdd3bf0dddc97b6df6b" + ] + ], + { + "versions_gcta": [ + [ + "GCTA_REMOVERELATEDSUBJECTS", + "gcta", + "1.94.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-15T22:50:50.597885689" + }, + "homo_sapiens popgen - remove related individuals from dense GRM - stub": { + "content": [ + [ + [ + { + "id": "stub_dense" + }, + [ + "stub_dense_unrel05.grm.N.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "stub_dense_unrel05.grm.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "stub_dense_unrel05.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + [ + { + "id": "stub_dense" + }, + "stub_dense_unrel05.grm.id:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + { + "versions_gcta": [ + [ + "GCTA_REMOVERELATEDSUBJECTS", + "gcta", + "1.94.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-15T22:55:53.542534458" + } +} \ No newline at end of file diff --git a/modules/nf-core/gcta/removerelatedsubjects/tests/nextflow.config b/modules/nf-core/gcta/removerelatedsubjects/tests/nextflow.config new file mode 100644 index 00000000000..de31e021882 --- /dev/null +++ b/modules/nf-core/gcta/removerelatedsubjects/tests/nextflow.config @@ -0,0 +1,3 @@ +params { + modules_testdata_base_path = System.getenv("NF_MODULES_TESTDATA_BASE_PATH") ?: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" +}