test: fixing the default nf-test

.github/workflows/nf-test.yml

@@ -66,13 +66,11 @@ jobs:
       fail-fast: false
       matrix:
         shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
-        profile: [conda, docker, singularity]
+        profile: [docker, singularity]
         isMain:
           - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         # Exclude conda and singularity on dev
         exclude:
-          - isMain: false
-            profile: "conda"
           - isMain: false
             profile: "singularity"
         NXF_VER:

.gitignore

@@ -1,4 +1,5 @@
 .nextflow*
+.nf-test*
 work/
 data/
 results/

CHANGELOG.md

@@ -32,6 +32,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt
 - Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected [#9](https://github.com/Clinical-Genomics/oncorefiner/pull/9)
 - Renamed pipeline from postprocessing to oncorefiner []()
 - Fixed linting issues [#20](https://github.com/Clinical-Genomics/oncorefiner/pull/20)
+- Fixed nf-test to run a functional default test, removed old CI test [#26](https://github.com/Clinical-Genomics/oncorefiner/pull/26)
 - Added missing description to bug_report.yml [32](https://github.com/Clinical-Genomics/oncorefiner/pull/32)
 - Updated template settings to set organisation to `Clinical-Genomics` and skip unused features `igenomes` and `fastqc` [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35)
 - Refactored `genome` parameter to have default value 'GRCh38' and no longer refer to igenomes [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35)

conf/modules/prepare_references.config

@@ -16,6 +16,13 @@
 //
 
 process {
+
+    withName: '.*:PREPARE_REFERENCES:.*' {
+        publishDir = [
+            enabled: false,
+        ]
+    }
+
     withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' {
         ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) }
     }

nextflow.config

@@ -186,8 +186,8 @@ profiles {
         apptainer.runOptions    = '--nv'
         singularity.runOptions  = '--nv'
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
+    test_full   { includeConfig 'conf/test_full.config'      }
+    test        { includeConfig 'conf/test.config'           }
 }
 
 // Load nf-core custom profiles from different institutions

nf-test.config

@@ -20,5 +20,6 @@ config {
     // load the necessary plugins
     plugins {
         load "nft-utils@0.0.3"
+        load "nft-vcf@1.0.7"
     }
 }

tests/.nftignore

@@ -7,4 +7,13 @@ multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+multiqc/multiqc_data/multiqc_citations.txt
 pipeline_info/*.{html,json,txt,yml}
+annotate_sv/*.{vcf.gz,tbi,html}
+vep/*.{vcf.gz,tbi,html}
+clinical/*.{vcf,vcf.gz,tbi}
+clinical_filtering/*.{vcf.gz,tbi}
+svdb/*.{vcf,vcf.gz,tbi}
+vcfanno/*.{vcf.gz,tbi}
+research/*.{vcf,vcf.gz,tbi}
+research_filtering/*.{vcf,vcf.gz,tbi}

tests/default.nf.test

@@ -1,6 +1,6 @@
 nextflow_pipeline {
 
-    name "Test pipeline"
+    name "Test pipeline ONCOREFINER"
     script "../main.nf"
     tag "pipeline"
 
@@ -17,6 +17,10 @@ nextflow_pipeline {
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // all_vcf_files: All vcf files - can have unstable variants and/or unstable headers
+            def all_vcf_files    = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
+            // vcfs_with_stable_variants: Vcf files with stable variants - can be snapshot using variantsMD5
+            def vcfs_with_stable_variants = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +29,11 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path
+                    stable_path,
+                    // All VCFs
+                    all_vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.summary ] },
+                    // VCFs with stable variants
+                    vcfs_with_stable_variants.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5 ] }
                 ).match() }
             )
         }

tests/default.nf.test.snap

@@ -0,0 +1,119 @@
+{
+    "-profile test": {
+        "content": [
+            {
+                "CLINICAL_FILTERING": {
+                    "bcftools": 1.22
+                },
+                "CLINICAL_FILTERING_SV": {
+                    "bcftools": 1.22
+                },
+                "ENSEMBLVEP_SNV": {
+                    "ensemblvep": 115.2,
+                    "perl-math-cdf": 0.1,
+                    "tabix": 1.21
+                },
+                "ENSEMBLVEP_SV": {
+                    "ensemblvep": 115.2,
+                    "perl-math-cdf": 0.1,
+                    "tabix": 1.21
+                },
+                "RESEARCH_FILTERING": {
+                    "bcftools": 1.22
+                },
+                "RESEARCH_FILTERING_SV": {
+                    "bcftools": 1.22
+                },
+                "SVDB_QUERY_DB": {
+                    "svdb": "2.8.4"
+                },
+                "UNTAR_VEP_CACHE": {
+                    "untar": 1.34
+                },
+                "VCFANNO": {
+                    "vcfanno": "0.3.7"
+                },
+                "Workflow": {
+                    "Clinical-Genomics/oncorefiner": "v1.0.0dev"
+                }
+            },
+            [
+                "annotate_sv",
+                "annotate_sv/SV_svdbquery_vep.vcf.gz",
+                "annotate_sv/SV_svdbquery_vep.vcf.gz.tbi",
+                "annotate_sv/SV_svdbquery_vep.vcf.gz_summary.html",
+                "clinical",
+                "clinical/SV_clinical.vcf",
+                "clinical_filtering",
+                "clinical_filtering/SNV_clinical.vcf.gz",
+                "pipeline_info",
+                "pipeline_info/oncorefiner_software_mqc_versions.yml",
+                "research",
+                "research/SV_research.vcf",
+                "research_filtering",
+                "research_filtering/SNV_research.vcf.gz",
+                "svdb",
+                "svdb/SV_vcfdb_query.vcf",
+                "vcfanno",
+                "vcfanno/SNV_vcfanno.vcf.gz",
+                "vcfanno/SNV_vcfanno.vcf.gz.tbi",
+                "vep",
+                "vep/SNV_vep.vcf.gz",
+                "vep/SNV_vep.vcf.gz.tbi",
+                "vep/SNV_vep.vcf.gz_summary.html"
+            ],
+            [
+
+            ],
+            [
+                [
+                    "SV_svdbquery_vep.vcf.gz",
+                    "VcfFile [chromosomes=[], sampleCount=2, variantCount=0, phased=true, phasedAutodetect=true]"
+                ],
+                [
+                    "SNV_clinical.vcf.gz",
+                    "VcfFile [chromosomes=[11, 22, 12, 13, 15, 16, 17, 18, 19, 1, 2, 3, 4, 5, 6, 7, 8, X, 9, 20, 21], sampleCount=2, variantCount=102, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "SNV_research.vcf.gz",
+                    "VcfFile [chromosomes=[11, 22, 12, 13, 15, 16, 17, 18, 19, 1, 2, 3, 4, 5, 6, 7, 8, X, 9, 20, 21], sampleCount=2, variantCount=102, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "SNV_vcfanno.vcf.gz",
+                    "VcfFile [chromosomes=[11, 22, 12, 13, 15, 16, 17, 18, 19, 1, 2, 3, 4, 5, 6, 7, 8, X, 9, 20, 21], sampleCount=2, variantCount=102, phased=false, phasedAutodetect=false]"
+                ],
+                [
+                    "SNV_vep.vcf.gz",
+                    "VcfFile [chromosomes=[11, 22, 12, 13, 15, 16, 17, 18, 19, 1, 2, 3, 4, 5, 6, 7, 8, X, 9, 20, 21], sampleCount=2, variantCount=102, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                [
+                    "SV_svdbquery_vep.vcf.gz",
+                    "d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                [
+                    "SNV_clinical.vcf.gz",
+                    "dd792f7ceac820af3fe366985474805"
+                ],
+                [
+                    "SNV_research.vcf.gz",
+                    "d7453d6080983d2c812113003f5e5ae8"
+                ],
+                [
+                    "SNV_vcfanno.vcf.gz",
+                    "746d273c13550ab044af7eb5e62a941a"
+                ],
+                [
+                    "SNV_vep.vcf.gz",
+                    "dd792f7ceac820af3fe366985474805"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-03-10T15:16:44.819454"
+    }
+}

tests/nextflow.config

@@ -2,13 +2,41 @@
 ========================================================================================
     Nextflow config file for running nf-test tests
 ========================================================================================
+ Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nf-test test tests/<test> --profile <test,docker>
+        nf-test test --profile=+test,docker
+
 */
 
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
 params {
-    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/refs/heads/oncorefiner'
+    config_profile_name          = 'Test profile'
+    config_profile_description   = 'Minimal test dataset to check pipeline function'
+    modules_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/tree/1184e1c31b5e47055e3580c7e0f65240a1c005d0/'
+
+
 }
 
-aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
+
+// Same Nextflow version as nextflow.config
+manifest {
+    nextflowVersion = '!>=25.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}