nf-core · atrigila · May 24, 2026 · May 24, 2026 · May 24, 2026 · May 24, 2026
diff --git 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 → tests/function.nf.test b/workflows/phaseimpute/tests/function.nf.test → 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/...s/phaseimpute/tests/function.nf.test.snap → tests/function.nf.test.snap b/...s/phaseimpute/tests/function.nf.test.snap → tests/function.nf.test.snap
diff --git 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
@@ -11,13 +11,53 @@ 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" }
         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 ]
+    }
+
 }
 
 // Or any resources requirements

diff --git a/tests/test_all.nf.test 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/...s/phaseimpute/tests/test_all.nf.test.snap → tests/test_all.nf.test.snap b/...s/phaseimpute/tests/test_all.nf.test.snap → tests/test_all.nf.test.snap
diff --git a/tests/test_batch.nf.test 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/...phaseimpute/tests/test_batch.nf.test.snap → tests/test_batch.nf.test.snap b/...phaseimpute/tests/test_batch.nf.test.snap → tests/test_batch.nf.test.snap
@@ -464,21 +464,35 @@
                 ]
             },
             {
-                "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"
                     ]
                 }
             }
         ],
-        "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
@@ -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/...aseimpute/tests/test_beagle5.nf.test.snap → tests/test_beagle5.nf.test.snap b/...aseimpute/tests/test_beagle5.nf.test.snap → tests/test_beagle5.nf.test.snap
diff --git a/tests/test_dog.nf.test 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("$outdir/imputation/quilt/concat/all_samples.batch0.quilt.vcf.gz"),
+                ]
+            },
+        ]
+    ]
+
+    test_scenario.each { scenario ->
+        test(scenario.name, UTILS.getPhaseimputeTest(scenario))
+    }
+}
diff --git a/...s/phaseimpute/tests/test_dog.nf.test.snap → tests/test_dog.nf.test.snap b/...s/phaseimpute/tests/test_dog.nf.test.snap → tests/test_dog.nf.test.snap
diff --git a/tests/test_glimpse1.nf.test b/tests/test_glimpse1.nf.test
@@ -0,0 +1,39 @@
+def projectDir = new File('.').absolutePath
+
+nextflow_pipeline {
+
+    name "Test phaseimpute workflow"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline/phaseimpute"
+    tag "test_glimpse1"
+
+    def test_scenario = [
+        [
+            name: "Check test_glimpse1 - with chunks - with map",
+            config: "../conf/test.config",
+            details: { outdir ->
+                [
+                    "all_samples.batch0.glimpse1": UTILS.vcfDetails("$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))
+    }
+}