diff --git a/CHANGELOG.md b/CHANGELOG.md index 279c9b75..34a92d89 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#294](https://github.com/nf-core/phaseimpute/pull/294) - Migrate nf-tests to `UTILS.groovy` structure. - [#267](https://github.com/nf-core/phaseimpute/pull/267) - Refactor repeated `params.steps` / `params.tools` and replace `println` calls with `log.info`. - [#244](https://github.com/nf-core/phaseimpute/pull/244) - Start migration to strict syntax. - [#237](https://github.com/nf-core/phaseimpute/pull/237) - Bump version to 1.2.0dev and update `CHANGELOG.md`. diff --git a/workflows/phaseimpute/tests/function.nf.test b/tests/function.nf.test similarity index 98% rename from workflows/phaseimpute/tests/function.nf.test rename to tests/function.nf.test index a91f217a..8ea3f311 100644 --- a/workflows/phaseimpute/tests/function.nf.test +++ b/tests/function.nf.test @@ -5,7 +5,7 @@ nextflow_function { */ name "Test function phaseimpute" - script "../function.nf" + script "../workflows/phaseimpute/function.nf" tag "function" test("Prepare chunks channel Glimpse - with chunks") { diff --git a/workflows/phaseimpute/tests/function.nf.test.snap b/tests/function.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/function.nf.test.snap rename to tests/function.nf.test.snap diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index d7b715c6..b3a7715d 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -45,4 +45,42 @@ class UTILS { def samples = path(filePath).vcf.header.getGenotypeSamples().sort() return [summary: summary, samples: samples] } + + + public static def getPhaseimputeTest = { Map scenario -> + return { + tag "pipeline" + tag "pipeline/phaseimpute" + + if (scenario.tag) { + tag scenario.tag + } + + config scenario.config + + when { + params { + publish_dir_mode = "copy" + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' + outdir = "$outputDir" + publish_all = true + + (scenario.params ?: [:]).each { key, value -> + delegate."$key" = value + } + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.getPipelineResults(outputDir, workflow), + *(scenario.details ? [scenario.details(outputDir)] : []) + ).match() } + ) + } + } + } + } diff --git a/tests/nextflow.config b/tests/nextflow.config index 8330c58b..e79c33bb 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -11,6 +11,39 @@ process { time: '2.h' ] + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:SHAPEIT5_PHASECOMMON' { + cpus = 1 + ext.args = { "--seed ${params.seed}" } + ext.suffix = "bcf" + ext.prefix = { "${meta.panel_id}_${meta.regionout.replace(':',"_")}_chunks" } + } + + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:STITCH' { + cpus = 1 + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.stitch" } + } + + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT:QUILT_QUILT' { + cpus = 1 + ext.args = { "--seed=${params.seed}" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt" } + } + + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:QUILT_QUILT2' { + cpus = 1 + ext.args = { "--seed=${params.seed} --use_mspbwt=TRUE --impute_rare_common=FALSE" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt2" } + } + + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:GLIMPSE2_PHASE' { + cpus = 1 + cache = "lenient" + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.glimpse2" } + ext.args = { "--keep-monomorphic-ref-sites --seed ${params.seed}" } + ext.suffix = "bcf" + publishDir = [ enabled: false ] + } + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE:GLIMPSE_PHASE' { cpus = 1 ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.glimpse1" } @@ -18,6 +51,13 @@ process { ext.suffix = "bcf" publishDir = [ enabled: false ] } + + withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BEAGLE5_BEAGLE' { + ext.args = { "gp=true ap=true seed=${params.seed}" } + ext.prefix = { "${meta.id}.${meta.chr}.beagle5" } + publishDir = [ enabled: false ] + } + } // Or any resources requirements diff --git a/tests/test_all.nf.test b/tests/test_all.nf.test new file mode 100644 index 00000000..15417c49 --- /dev/null +++ b/tests/test_all.nf.test @@ -0,0 +1,44 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_all" + + def test_scenario = [ + [ + name: "Check test_all - with map", + config: "../conf/test_all.config", + details: { outdir -> + [ + "all_samples.glimpse1": UTILS.vcfDetails("$outdir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), + "all_samples.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + "all_samples.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + "all_samples.stitch": UTILS.vcfDetails("$outdir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz"), + ] + }, + ], + [ + name: "Check test_all - no map", + config: "../conf/test_all.config", + params: [ + map: null, + ], + details: { outdir -> + [ + "all_samples.glimpse1": UTILS.vcfDetails("$outdir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), + "all_samples.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + "all_samples.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + "all_samples.stitch": UTILS.vcfDetails("$outdir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_all.nf.test.snap b/tests/test_all.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_all.nf.test.snap rename to tests/test_all.nf.test.snap diff --git a/tests/test_batch.nf.test b/tests/test_batch.nf.test new file mode 100644 index 00000000..5e0ba8b3 --- /dev/null +++ b/tests/test_batch.nf.test @@ -0,0 +1,29 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_batch" + + def test_scenario = [ + [ + name: "Check test_batch", + config: "../conf/test_batch.config", + details: { outdir -> + [ + "all_samples.batch0.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + "all_samples.batch1.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch1.glimpse2.vcf.gz"), + "all_samples.batch0.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + "all_samples.batch1.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch1.quilt.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_batch.nf.test.snap b/tests/test_batch.nf.test.snap similarity index 97% rename from workflows/phaseimpute/tests/test_batch.nf.test.snap rename to tests/test_batch.nf.test.snap index a8fb8961..58b5f58a 100644 --- a/workflows/phaseimpute/tests/test_batch.nf.test.snap +++ b/tests/test_batch.nf.test.snap @@ -464,13 +464,27 @@ ] }, { - "all_samples.glimpse2": { + "all_samples.batch0.glimpse2": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=2, variantCount=1739, phased=true]", + "samples": [ + "NA12878", + "NA19401" + ] + }, + "all_samples.batch1.glimpse2": { "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=1, variantCount=1739, phased=true]", "samples": [ "NA20359" ] }, - "all_samples.quilt": { + "all_samples.batch0.quilt": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=2, variantCount=1739, phased=true]", + "samples": [ + "NA12878", + "NA19401" + ] + }, + "all_samples.batch1.quilt": { "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=1, variantCount=1739, phased=true]", "samples": [ "NA20359" @@ -478,7 +492,7 @@ } } ], - "timestamp": "2026-05-17T14:05:55.670301894", + "timestamp": "2026-05-24T16:25:40.025066728", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/test_beagle5.nf.test b/tests/test_beagle5.nf.test new file mode 100644 index 00000000..7b5c9c68 --- /dev/null +++ b/tests/test_beagle5.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_beagle5" + + def test_scenario = [ + [ + name: "Check test_beagle5 - with chunks - with map", + config: "../conf/test_beagle5.config", + details: { outdir -> + [ + "NA12878.beagle5": UTILS.vcfDetails("$outdir/imputation/beagle5/concat/NA12878.beagle5.vcf.gz"), + ] + }, + ], + [ + name: "Check test_beagle5 - no chunks - no map", + config: "../conf/test_beagle5.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "NA12878.beagle5": UTILS.vcfDetails("$outdir/imputation/beagle5/concat/NA12878.beagle5.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test.snap b/tests/test_beagle5.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_beagle5.nf.test.snap rename to tests/test_beagle5.nf.test.snap diff --git a/tests/test_dog.nf.test b/tests/test_dog.nf.test new file mode 100644 index 00000000..b81ff15b --- /dev/null +++ b/tests/test_dog.nf.test @@ -0,0 +1,28 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_dog" + + def test_scenario = [ + [ + name: "Check test_dog - no map", + config: "../conf/test_dog.config", + details: { outdir -> + [ + "all_samples.glimpse1": UTILS.vcfDetails("$outdir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), + "all_samples.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + "all_samples.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_dog.nf.test.snap b/tests/test_dog.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_dog.nf.test.snap rename to tests/test_dog.nf.test.snap diff --git a/tests/test_glimpse1.nf.test b/tests/test_glimpse1.nf.test new file mode 100644 index 00000000..567dbf25 --- /dev/null +++ b/tests/test_glimpse1.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_glimpse1" + + def test_scenario = [ + [ + name: "Check test_glimpse1 - with chunks - with map", + config: "../conf/test.config", + details: { outdir -> + [ + "all_samples.batch0.glimpse1": UTILS.vcfDetails("$outdir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), + ] + }, + ], + [ + name: "Check test_glimpse1 - no chunks - no map", + config: "../conf/test.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "all_samples.batch0.glimpse1": UTILS.vcfDetails("$outdir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/tests/test_glimpse1.nf.test.snap b/tests/test_glimpse1.nf.test.snap new file mode 100644 index 00000000..a0ac43a4 --- /dev/null +++ b/tests/test_glimpse1.nf.test.snap @@ -0,0 +1,618 @@ +{ + "Check test_glimpse1 - no chunks - no map": { + "content": [ + { + "workflow size": 35, + "versions": { + "BAMCHREXTRACT": { + "samtools": "1.23" + }, + "BCFTOOLS_ANNOTATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_CONCAT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_LIGATE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_INDEX_PHASE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_MERGE": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_MPILEUP": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_PLUGINSPLIT": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_QUERY_IMPUTED": { + "bcftools": "1.23.1" + }, + "BCFTOOLS_STATS_TOOLS": { + "bcftools": "1.23.1" + }, + "GAWK_IMPUTED": { + "gawk": "5.3.1" + }, + 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"all_samples.batch0.chr22.ligate.glimpse1.vcf.gz", + "ee5dcc24589467890db44fdbae04c161" + ], + [ + "NA12878.glimpse1.vcf.gz", + "223a9b6ea48ff9c11215bf9c00c8dbcb" + ], + [ + "NA19401.glimpse1.vcf.gz", + "34dbf34cde4412b1327a72fb8eb14e6f" + ], + [ + "NA20359.glimpse1.vcf.gz", + "bd4fde5baf064d7a88c513d6ba3cb62a" + ], + [ + "NA12878_chr21.vcf.gz", + "4198ecfcd59029b10716f2c033f96343" + ], + [ + "NA12878_chr22.vcf.gz", + "2de6a606cb5ae4284b979fc00934302f" + ], + [ + "NA19401_chr21.vcf.gz", + "307139605cffb09295b27619d1e3cf41" + ], + [ + "NA19401_chr22.vcf.gz", + "7d45992def27887e96cd859480189509" + ], + [ + "NA20359_chr21.vcf.gz", + "1cca23409d5074b28e41fcda7f978021" + ], + [ + "NA20359_chr22.vcf.gz", + "a4888d2aa2af452d115f70a58ebfb8f4" + ], + [ + "all_samples.annotate.vcf.gz", + "b9a7c83f719a9c3a3d8a39cf5f302a9d" + ], + [ + "all_samples.concat.vcf.gz", + "e6f43808fd6787f348d7614bbda9b333" + ], + [ + "all_samples_chr21.merge.vcf.gz", + "8aa42728d938b7f47130497b4dc86955" + ], + [ + "all_samples_chr22.merge.vcf.gz", + "170d05c06240dceb6f079c70b1e234e3" + ] + ], + "CSV files": [ + { + "fileName": "impute.csv", + "rows": [ + "sample,tools,file,index", + "NA12878,glimpse1,NA12878.glimpse1.vcf.gz,NA12878.glimpse1.vcf.gz.tbi", + "NA19401,glimpse1,NA19401.glimpse1.vcf.gz,NA19401.glimpse1.vcf.gz.tbi", + "NA20359,glimpse1,NA20359.glimpse1.vcf.gz,NA20359.glimpse1.vcf.gz.tbi" + ] + } + ] + }, + { + "all_samples.batch0.glimpse1": { + "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", + "samples": [ + "NA12878", + "NA19401", + "NA20359" + ] + } + } + ], + "timestamp": "2026-05-17T15:36:32.947739141", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } + } +} diff --git a/tests/test_glimpse2.nf.test b/tests/test_glimpse2.nf.test new file mode 100644 index 00000000..8e732c56 --- /dev/null +++ b/tests/test_glimpse2.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_glimpse2" + + def test_scenario = [ + [ + name: "Check test_glimpse2 - with chunks - with map", + config: "../conf/test_glimpse2.config", + details: { outdir -> + [ + "all_samples.batch0.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + ] + }, + ], + [ + name: "Check test_glimpse2 - no chunks - no map", + config: "../conf/test_glimpse2.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "all_samples.batch0.glimpse2": UTILS.vcfDetails("$outdir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_glimpse2.nf.test.snap b/tests/test_glimpse2.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_glimpse2.nf.test.snap rename to tests/test_glimpse2.nf.test.snap diff --git a/tests/test_minimac4.nf.test b/tests/test_minimac4.nf.test new file mode 100644 index 00000000..e7a10b52 --- /dev/null +++ b/tests/test_minimac4.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_minimac4" + + def test_scenario = [ + [ + name: "Check test_minimac4 - with chunks - with map", + config: "../conf/test_minimac4.config", + details: { outdir -> + [ + "NA12878.minimac4": UTILS.vcfDetails("$outdir/imputation/minimac4/concat/NA12878.minimac4.vcf.gz"), + ] + }, + ], + [ + name: "Check test_minimac4 - no chunks - no map", + config: "../conf/test_minimac4.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "NA12878.minimac4": UTILS.vcfDetails("$outdir/imputation/minimac4/concat/NA12878.minimac4.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_minimac4.nf.test.snap b/tests/test_minimac4.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_minimac4.nf.test.snap rename to tests/test_minimac4.nf.test.snap diff --git a/tests/test_panelprep.nf.test b/tests/test_panelprep.nf.test new file mode 100644 index 00000000..63fa91d0 --- /dev/null +++ b/tests/test_panelprep.nf.test @@ -0,0 +1,31 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_panelprep" + + def test_scenario = [ + [ + name: "Check test_panelprep - with chunks - with map", + config: "../conf/test_panelprep.config", + params: [ + chunks: "${projectDir}/tests/csv/chunks.csv", + ], + ], + [ + name: "Check test_panelprep - no chunks - no map", + config: "../conf/test_panelprep.config", + params: [ + map: null, + ], + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_panelprep.nf.test.snap b/tests/test_panelprep.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_panelprep.nf.test.snap rename to tests/test_panelprep.nf.test.snap diff --git a/tests/test_quilt.nf.test b/tests/test_quilt.nf.test new file mode 100644 index 00000000..4926d3d2 --- /dev/null +++ b/tests/test_quilt.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_quilt" + + def test_scenario = [ + [ + name: "Check test_quilt - with chunks - with map", + config: "../conf/test_quilt.config", + details: { outdir -> + [ + "all_samples.batch0.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + ] + }, + ], + [ + name: "Check test_quilt - no chunks - no map", + config: "../conf/test_quilt.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "all_samples.batch0.quilt": UTILS.vcfDetails("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_quilt.nf.test.snap b/tests/test_quilt.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_quilt.nf.test.snap rename to tests/test_quilt.nf.test.snap diff --git a/tests/test_quilt2.nf.test b/tests/test_quilt2.nf.test new file mode 100644 index 00000000..8fd9ebb6 --- /dev/null +++ b/tests/test_quilt2.nf.test @@ -0,0 +1,50 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_quilt2" + + def test_scenario = [ + [ + name: "Check test_quilt2 - with chunks - with map", + config: "../conf/test_quilt2.config", + details: { outdir -> + [ + "all_samples.batch0.quilt2": UTILS.vcfDetails("$outdir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz"), + ] + }, + ], + [ + name: "Check test_quilt2 - with chunks - no map", + config: "../conf/test_quilt2.config", + params: [ + map: null, + ], + details: { outdir -> + [ + "all_samples.batch0.quilt2": UTILS.vcfDetails("$outdir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz"), + ] + }, + ], + [ + name: "Check test_quilt2 - no chunks - with map", + config: "../conf/test_quilt2.config", + params: [ + chunks: null, + ], + details: { outdir -> + [ + "all_samples.batch0.quilt2": UTILS.vcfDetails("$outdir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_quilt2.nf.test.snap b/tests/test_quilt2.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_quilt2.nf.test.snap rename to tests/test_quilt2.nf.test.snap diff --git a/tests/test_sim.nf.test b/tests/test_sim.nf.test new file mode 100644 index 00000000..b610c51f --- /dev/null +++ b/tests/test_sim.nf.test @@ -0,0 +1,21 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_sim" + + def test_scenario = [ + [ + name: "Check test_sim", + config: "../conf/test_sim.config", + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_sim.nf.test.snap b/tests/test_sim.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_sim.nf.test.snap rename to tests/test_sim.nf.test.snap diff --git a/tests/test_stitch.nf.test b/tests/test_stitch.nf.test new file mode 100644 index 00000000..2a6a9336 --- /dev/null +++ b/tests/test_stitch.nf.test @@ -0,0 +1,39 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_stitch" + + def test_scenario = [ + [ + name: "Check test_stitch - with chunks - with map", + config: "../conf/test_stitch.config", + details: { outdir -> + [ + "all_samples.batch0.stitch": UTILS.vcfDetails("$outdir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz"), + ] + }, + ], + [ + name: "Check test_stitch - no chunks - no map", + config: "../conf/test_stitch.config", + params: [ + chunks: null, + map: null, + ], + details: { outdir -> + [ + "all_samples.batch0.stitch": UTILS.vcfDetails("$outdir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz"), + ] + }, + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_stitch.nf.test.snap b/tests/test_stitch.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_stitch.nf.test.snap rename to tests/test_stitch.nf.test.snap diff --git a/tests/test_validate.nf.test b/tests/test_validate.nf.test new file mode 100644 index 00000000..d147294d --- /dev/null +++ b/tests/test_validate.nf.test @@ -0,0 +1,21 @@ +def projectDir = new File('.').absolutePath + +nextflow_pipeline { + + name "Test phaseimpute workflow" + script "../main.nf" + tag "pipeline" + tag "pipeline/phaseimpute" + tag "test_validate" + + def test_scenario = [ + [ + name: "Check test_validate", + config: "../conf/test_validate.config", + ] + ] + + test_scenario.each { scenario -> + test(scenario.name, UTILS.getPhaseimputeTest(scenario)) + } +} diff --git a/workflows/phaseimpute/tests/test_validate.nf.test.snap b/tests/test_validate.nf.test.snap similarity index 100% rename from workflows/phaseimpute/tests/test_validate.nf.test.snap rename to tests/test_validate.nf.test.snap diff --git a/workflows/phaseimpute/tests/nextflow.config b/workflows/phaseimpute/tests/nextflow.config deleted file mode 100644 index adb9f70c..00000000 --- a/workflows/phaseimpute/tests/nextflow.config +++ /dev/null @@ -1,48 +0,0 @@ -process { - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:SHAPEIT5_PHASECOMMON' { - cpus = 1 - ext.args = {"--seed ${params.seed}"} - ext.suffix = "bcf" - ext.prefix = { "${meta.panel_id}_${meta.regionout.replace(':',"_")}_chunks" } - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:STITCH' { - cpus = 1 - ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.stitch" } - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT:QUILT_QUILT' { - cpus = 1 - ext.args = {"--seed=${params.seed}" } - ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt" } - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:QUILT_QUILT2' { - cpus = 1 - ext.args = {"--seed=${params.seed} --use_mspbwt=TRUE --impute_rare_common=FALSE" } - ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt2" } - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:GLIMPSE2_PHASE' { - cpus = 1 - cache = "lenient" - ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.glimpse2" } - ext.args = { "--keep-monomorphic-ref-sites --seed ${params.seed}" } - ext.suffix = "bcf" - publishDir = [ enabled: false ] - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE:GLIMPSE_PHASE' { - cpus = 1 - ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.glimpse1" } - ext.args = { "--impute-reference-only-variants --seed ${params.seed}" } - ext.suffix = "bcf" - publishDir = [ enabled: false ] - } - - withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BEAGLE5_BEAGLE' { - ext.args = { "gp=true ap=true seed=${params.seed}" } - ext.prefix = { "${meta.id}.${meta.chr}.beagle5" } - publishDir = [ enabled: false ] - } -} diff --git a/workflows/phaseimpute/tests/test_all.nf.test b/workflows/phaseimpute/tests/test_all.nf.test deleted file mode 100644 index 0c48dbe7..00000000 --- a/workflows/phaseimpute/tests/test_all.nf.test +++ /dev/null @@ -1,65 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_all" - - config "./nextflow.config" - - test("Check test_all - with map") { - config "../../../conf/test_all.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - [ - "all_samples.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), - "all_samples.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), - "all_samples.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), - "all_samples.stitch": UTILS.vcfDetails("$outputDir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz") - ] - ).match()} - ) - } - } - - test("Check test_all - no map") { - config "../../../conf/test_all.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - map = null - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - [ - "all_samples.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), - "all_samples.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), - "all_samples.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), - "all_samples.stitch": UTILS.vcfDetails("$outputDir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz") - ] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_batch.nf.test b/workflows/phaseimpute/tests/test_batch.nf.test deleted file mode 100644 index c063d216..00000000 --- a/workflows/phaseimpute/tests/test_batch.nf.test +++ /dev/null @@ -1,38 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - - tag "test_batch" - - config "./nextflow.config" - - test("Check test_batch") { - config "../../../conf/test_batch.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - [ - "all_samples.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), - "all_samples.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch1.glimpse2.vcf.gz"), - "all_samples.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"), - "all_samples.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch1.quilt.vcf.gz") - ] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_beagle5.nf.test b/workflows/phaseimpute/tests/test_beagle5.nf.test deleted file mode 100644 index c045e6d0..00000000 --- a/workflows/phaseimpute/tests/test_beagle5.nf.test +++ /dev/null @@ -1,56 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_beagle5" - - config "./nextflow.config" - - test("Check test_beagle5 - with chunks - with map") { - config "../../../conf/test_beagle5.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["NA12878.beagle5": UTILS.vcfDetails("$outputDir/imputation/beagle5/concat/NA12878.beagle5.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_beagle5 - no chunks - no map") { - config "../../../conf/test_beagle5.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["NA12878.beagle5": UTILS.vcfDetails("$outputDir/imputation/beagle5/concat/NA12878.beagle5.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_dog.nf.test b/workflows/phaseimpute/tests/test_dog.nf.test deleted file mode 100644 index d43d55d8..00000000 --- a/workflows/phaseimpute/tests/test_dog.nf.test +++ /dev/null @@ -1,36 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_dog" - - config "./nextflow.config" - - test("Check test_dog - no map") { - config "../../../conf/test_dog.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - [ - "all_samples.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz"), - "all_samples.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz"), - "all_samples.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz") - ] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_glimpse1.nf.test b/workflows/phaseimpute/tests/test_glimpse1.nf.test deleted file mode 100644 index f5059215..00000000 --- a/workflows/phaseimpute/tests/test_glimpse1.nf.test +++ /dev/null @@ -1,56 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_glimpse1" - - config "./nextflow.config" - - test("Check test_glimpse1 - with chunks - with map") { - config "../../../conf/test.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_glimpse1 - no chunks - no map") { - config "../../../conf/test.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.glimpse1": UTILS.vcfDetails("$outputDir/imputation/glimpse1/concat/all_samples.batch0.glimpse1.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap b/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap deleted file mode 100644 index dde14b51..00000000 --- a/workflows/phaseimpute/tests/test_glimpse1.nf.test.snap +++ /dev/null @@ -1,1502 +0,0 @@ -{ - "Check test_glimpse1 - no chunks - no map": { - "content": [ - { - "workflow size": 35, - "versions": { - "BAMCHREXTRACT": { - "samtools": "1.23" - }, - "BCFTOOLS_ANNOTATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_CONCAT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_LIGATE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_INDEX_PHASE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_MERGE": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_MPILEUP": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_PLUGINSPLIT": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_QUERY_IMPUTED": { - "bcftools": "1.23.1" - }, - "BCFTOOLS_STATS_TOOLS": { - "bcftools": "1.23.1" - }, - "GAWK_IMPUTED": { - "gawk": "5.3.1" - }, - "GLIMPSE_LIGATE": { - "glimpse": "1.1.1" - }, - "GLIMPSE_PHASE": { - "glimpse": "1.1.1" - }, - "LISTTOFILE": { - "gawk": "5.3.1" - }, - "SAMTOOLS_FAIDX": { - "samtools": "1.23.1" - }, - "TABIX_TABIX": { - "tabix": "1.21" 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"NA19401,glimpse1,NA19401.glimpse1.vcf.gz,NA19401.glimpse1.vcf.gz.tbi", - "NA20359,glimpse1,NA20359.glimpse1.vcf.gz,NA20359.glimpse1.vcf.gz.tbi" - ] - } - ] - }, - { - "all_samples.batch0.glimpse1": { - "summary": "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]", - "samples": [ - "NA12878", - "NA19401", - "NA20359" - ] - } - } - ], - "timestamp": "2026-05-17T15:36:32.947739141", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.0" - } - } -} \ No newline at end of file diff --git a/workflows/phaseimpute/tests/test_glimpse2.nf.test b/workflows/phaseimpute/tests/test_glimpse2.nf.test deleted file mode 100644 index 2c9f2adc..00000000 --- a/workflows/phaseimpute/tests/test_glimpse2.nf.test +++ /dev/null @@ -1,56 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_glimpse2" - - config "./nextflow.config" - - test("Check test_glimpse2 - with chunks - with map") { - config "../../../conf/test_glimpse2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_glimpse2 - no chunks - no map") { - config "../../../conf/test_glimpse2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.glimpse2": UTILS.vcfDetails("$outputDir/imputation/glimpse2/concat/all_samples.batch0.glimpse2.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_minimac4.nf.test b/workflows/phaseimpute/tests/test_minimac4.nf.test deleted file mode 100644 index 90ff5642..00000000 --- a/workflows/phaseimpute/tests/test_minimac4.nf.test +++ /dev/null @@ -1,56 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_minimac4" - - config "./nextflow.config" - - test("Check test_minimac4 - with chunks - with map") { - config "../../../conf/test_minimac4.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["NA12878.minimac4": UTILS.vcfDetails("$outputDir/imputation/minimac4/concat/NA12878.minimac4.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_minimac4 - no chunks - no map") { - config "../../../conf/test_minimac4.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["NA12878.minimac4": UTILS.vcfDetails("$outputDir/imputation/minimac4/concat/NA12878.minimac4.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_panelprep.nf.test b/workflows/phaseimpute/tests/test_panelprep.nf.test deleted file mode 100644 index 6e3240c0..00000000 --- a/workflows/phaseimpute/tests/test_panelprep.nf.test +++ /dev/null @@ -1,55 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_panelprep" - - config "./nextflow.config" - - - test("Check test_panelprep - with chunks - with map") { - config "../../../conf/test_panelprep.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = "${projectDir}/tests/csv/chunks.csv" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow) - ).match()} - ) - } - } - - test("Check test_panelprep - no chunks - no map") { - config "../../../conf/test_panelprep.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow) - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_quilt.nf.test b/workflows/phaseimpute/tests/test_quilt.nf.test deleted file mode 100644 index f2c73f30..00000000 --- a/workflows/phaseimpute/tests/test_quilt.nf.test +++ /dev/null @@ -1,57 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_quilt" - - config "./nextflow.config" - - test("Check test_quilt - with chunks - with map") { - config "../../../conf/test_quilt.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_quilt - no chunks - no map") { - config "../../../conf/test_quilt.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt": UTILS.vcfDetails("$outputDir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_quilt2.nf.test b/workflows/phaseimpute/tests/test_quilt2.nf.test deleted file mode 100644 index bdd2defe..00000000 --- a/workflows/phaseimpute/tests/test_quilt2.nf.test +++ /dev/null @@ -1,79 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_quilt2" - - config "./nextflow.config" - - test("Check test_quilt2 - with chunks - with map") { - config "../../../conf/test_quilt2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt2": UTILS.vcfDetails("$outputDir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_quilt2 - with chunks - no map") { - config "../../../conf/test_quilt2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt2": UTILS.vcfDetails("$outputDir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_quilt2 - no chunks - with map") { - config "../../../conf/test_quilt2.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.quilt2": UTILS.vcfDetails("$outputDir/imputation/quilt2/concat/all_samples.batch0.quilt2.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_sim.nf.test b/workflows/phaseimpute/tests/test_sim.nf.test deleted file mode 100644 index f0af0773..00000000 --- a/workflows/phaseimpute/tests/test_sim.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_sim" - - config "./nextflow.config" - - test("Check test_sim") { - config "../../../conf/test_sim.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow) - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_stitch.nf.test b/workflows/phaseimpute/tests/test_stitch.nf.test deleted file mode 100644 index f9c07496..00000000 --- a/workflows/phaseimpute/tests/test_stitch.nf.test +++ /dev/null @@ -1,57 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_stitch" - - config "./nextflow.config" - - test("Check test_stitch - with chunks - with map") { - config "../../../conf/test_stitch.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.stitch": UTILS.vcfDetails("$outputDir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz")] - ).match()} - ) - } - } - - test("Check test_stitch - no chunks - no map") { - config "../../../conf/test_stitch.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - chunks = null - map = null - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow), - ["all_samples.batch0.stitch": UTILS.vcfDetails("$outputDir/imputation/stitch/concat/all_samples.batch0.stitch.vcf.gz")] - ).match()} - ) - } - } -} diff --git a/workflows/phaseimpute/tests/test_validate.nf.test b/workflows/phaseimpute/tests/test_validate.nf.test deleted file mode 100644 index 6db5edbb..00000000 --- a/workflows/phaseimpute/tests/test_validate.nf.test +++ /dev/null @@ -1,32 +0,0 @@ -nextflow_pipeline { - - name "Test phaseimpute workflow" - script "main.nf" - tag "pipeline" - tag "pipeline/phaseimpute" - tag "test_validate" - - config "./nextflow.config" - - test("Check test_validate") { - config "../../../conf/test_validate.config" - when { - params { - publish_dir_mode = "copy" - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/' - outdir = "$outputDir" - publish_all = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.getPipelineResults(outputDir, workflow) - ).match() } - ) - } - - } -}