rename + bcfann

tests/annotation_bcfann.nf.test

@@ -0,0 +1,40 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --tools bcfann") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
+                step  = 'annotate'
+                tools = 'bcfann'
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}

tests/annotation_bcfann.nf.test.snap

@@ -0,0 +1,40 @@
+{
+    "Run with profile test | --tools bcfann": {
+        "content": [
+            2,
+            {
+                "BCFTOOLS_ANNOTATE": {
+                    "bcftools": 1.2
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "annotation",
+                "annotation/test",
+                "annotation/test/test_BCF.ann.vcf.gz",
+                "annotation/test/test_BCF.ann.vcf.gz.tbi",
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T09:38:54.991004"
+    }
+}

tests/config/pytesttags.yml

@@ -441,14 +441,6 @@ tiddit:
 
 # annotate
 
-## cache
-cache:
-  - conf/modules/prepare_cache.config
-  - modules/nf-core/ensemblvep/download/**
-  - modules/nf-core/snpeff/download/**
-  - subworkflows/local/prepare_cache/**
-  - tests/test_annotation_cache.yml
-
 ## merge
 merge:
   - conf/modules/annotate.config
@@ -461,15 +453,6 @@ merge:
   - tests/csv/3.0/vcf_single.csv
   - tests/test_annotation_merge.yml
 
-## bcfann
-bcfann:
-  - conf/modules/annotate.config
-  - modules/nf-core/bcftools/annotate/**
-  - modules/nf-core/tabix/bgziptabix/**
-  - subworkflows/nf-core/vcf_annotate_bcftools/**
-  - tests/csv/3.0/vcf_single.csv
-  - tests/test_annotation_bcfann.yml
-
 # postprocessing
 
 ## concatenate germline vcfs