From 565ef201c74b04014c71b4e002bdcf35e4afb79e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 29 Oct 2024 10:22:00 +0100
Subject: [PATCH] add merge + refactor snpeff/vep

---
 tests/.nftignore                     |   2 +
 tests/annotation_merge.nf.test       |  77 ++++++++++
 tests/annotation_merge.nf.test.snap  | 205 +++++++++++++++++++++++++++
 tests/annotation_snpeff.nf.test      |  34 -----
 tests/annotation_snpeff.nf.test.snap |  91 +-----------
 tests/annotation_vep.nf.test         |  36 +----
 tests/annotation_vep.nf.test.snap    |  64 +--------
 tests/config/pytesttags.yml          |  14 --
 tests/test_annotation_merge.yml      |  58 --------
 9 files changed, 290 insertions(+), 291 deletions(-)
 create mode 100644 tests/annotation_merge.nf.test
 create mode 100644 tests/annotation_merge.nf.test.snap
 delete mode 100644 tests/test_annotation_merge.yml

diff --git a/tests/.nftignore b/tests/.nftignore
index b051a8987f..6996d5ea9c 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -18,4 +18,6 @@ reference/dragmap/hash_table_stats.txt
 reports/EnsemblVEP/*/*.ann.summary.html
 reports/fastqc/**/*_fastqc.{html,zip}
 reports/markduplicates/**/*.md.cram.metrics
+reports/snpeff/*/*_snpEff.csv
+reports/snpeff/*/snpEff_summary.html
 variant_calling/**/*.vcf.{gz,gz.tbi}
diff --git a/tests/annotation_merge.nf.test b/tests/annotation_merge.nf.test
new file mode 100644
index 0000000000..323b29eb3a
--- /dev/null
+++ b/tests/annotation_merge.nf.test
@@ -0,0 +1,77 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --tools merge") {
+
+        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'
+                snpeff_cache = 's3://annotation-cache/snpeff_cache/'
+                vep_cache = 's3://annotation-cache/vep_cache/'
+                tools = 'merge'
+            }
+        }
+
+        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() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools merge,snpeff,vep") {
+
+        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'
+                snpeff_cache = 's3://annotation-cache/snpeff_cache/'
+                vep_cache = 's3://annotation-cache/vep_cache/'
+                tools = 'merge,snpeff,vep'
+            }
+        }
+
+        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() }
+            )
+        }
+    }
+}
diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap
new file mode 100644
index 0000000000..4856da93f6
--- /dev/null
+++ b/tests/annotation_merge.nf.test.snap
@@ -0,0 +1,205 @@
+{
+    "Run with profile test | --tools merge,snpeff,vep": {
+        "content": [
+            7,
+            {
+                "ENSEMBLVEP_VEP": {
+                    "ensemblvep": 113.0
+                },
+                "SNPEFF_SNPEFF": {
+                    "snpeff": "5.1d"
+                },
+                "TABIX_BGZIPTABIX": {
+                    "tabix": 1.2
+                },
+                "TABIX_TABIX": {
+                    "tabix": 1.2
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "annotation",
+                "annotation/test",
+                "annotation/test/test_VEP.ann.vcf.gz",
+                "annotation/test/test_VEP.ann.vcf.gz.tbi",
+                "annotation/test/test_snpEff.ann.vcf.gz",
+                "annotation/test/test_snpEff.ann.vcf.gz.tbi",
+                "annotation/test/test_snpEff_VEP.ann.vcf.gz",
+                "annotation/test/test_snpEff_VEP.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_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_snpeff.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_data/snpeff_effects.txt",
+                "multiqc/multiqc_data/snpeff_qualities.txt",
+                "multiqc/multiqc_data/snpeff_variant_effects_region.txt",
+                "multiqc/multiqc_data/vep-general-stats.txt",
+                "multiqc/multiqc_data/vep.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_effects-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_effects-pct.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_qualities.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-log.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct-log.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct.pdf",
+                "multiqc/multiqc_plots/pdf/vep-general-stats.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/png/snpeff_effects-cnt.png",
+                "multiqc/multiqc_plots/png/snpeff_effects-pct.png",
+                "multiqc/multiqc_plots/png/snpeff_qualities.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-cnt.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-log.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct-log.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct.png",
+                "multiqc/multiqc_plots/png/vep-general-stats.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/multiqc_plots/svg/snpeff_effects-cnt.svg",
+                "multiqc/multiqc_plots/svg/snpeff_effects-pct.svg",
+                "multiqc/multiqc_plots/svg/snpeff_qualities.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-cnt.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-log.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct-log.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct.svg",
+                "multiqc/multiqc_plots/svg/vep-general-stats.svg",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reports",
+                "reports/EnsemblVEP",
+                "reports/EnsemblVEP/test",
+                "reports/EnsemblVEP/test/test_VEP.ann.summary.html",
+                "reports/EnsemblVEP/test/test_snpEff_VEP.ann.summary.html",
+                "reports/snpeff",
+                "reports/snpeff/test",
+                "reports/snpeff/test/snpEff_summary.html",
+                "reports/snpeff/test/test_snpEff.csv",
+                "reports/snpeff/test/test_snpEff.genes.txt"
+            ],
+            [
+                "multiqc_citations.txt:md5,ebf9f49bc020eeb38546ddab3a98171e",
+                "multiqc_snpeff.txt:md5,03a2b1c461cb6e5cccac64033a2f6526",
+                "snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
+                "snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
+                "snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
+                "vep-general-stats.txt:md5,71c994ae4221384f4e22459723d29cd0",
+                "vep.txt:md5,20570f3e4e51407b860a31d7e1d59de0",
+                "test_snpEff.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T10:03:16.229715"
+    },
+    "Run with profile test | --tools merge": {
+        "content": [
+            5,
+            {
+                "ENSEMBLVEP_VEP": {
+                    "ensemblvep": 113.0
+                },
+                "SNPEFF_SNPEFF": {
+                    "snpeff": "5.1d"
+                },
+                "TABIX_BGZIPTABIX": {
+                    "tabix": 1.2
+                },
+                "TABIX_TABIX": {
+                    "tabix": 1.2
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "annotation",
+                "annotation/test",
+                "annotation/test/test_snpEff_VEP.ann.vcf.gz",
+                "annotation/test/test_snpEff_VEP.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_general_stats.txt",
+                "multiqc/multiqc_data/multiqc_snpeff.txt",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_data/snpeff_effects.txt",
+                "multiqc/multiqc_data/snpeff_qualities.txt",
+                "multiqc/multiqc_data/snpeff_variant_effects_region.txt",
+                "multiqc/multiqc_data/vep-general-stats.txt",
+                "multiqc/multiqc_data/vep.txt",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_effects-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_effects-pct.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_qualities.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-log.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct-log.pdf",
+                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct.pdf",
+                "multiqc/multiqc_plots/pdf/vep-general-stats.pdf",
+                "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/general_stats_table.png",
+                "multiqc/multiqc_plots/png/snpeff_effects-cnt.png",
+                "multiqc/multiqc_plots/png/snpeff_effects-pct.png",
+                "multiqc/multiqc_plots/png/snpeff_qualities.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-cnt.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-log.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct-log.png",
+                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct.png",
+                "multiqc/multiqc_plots/png/vep-general-stats.png",
+                "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/general_stats_table.svg",
+                "multiqc/multiqc_plots/svg/snpeff_effects-cnt.svg",
+                "multiqc/multiqc_plots/svg/snpeff_effects-pct.svg",
+                "multiqc/multiqc_plots/svg/snpeff_qualities.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-cnt.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-log.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct-log.svg",
+                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct.svg",
+                "multiqc/multiqc_plots/svg/vep-general-stats.svg",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reports",
+                "reports/EnsemblVEP",
+                "reports/EnsemblVEP/test",
+                "reports/EnsemblVEP/test/test_snpEff_VEP.ann.summary.html",
+                "reports/snpeff",
+                "reports/snpeff/test"
+            ],
+            [
+                "multiqc_citations.txt:md5,ebf9f49bc020eeb38546ddab3a98171e",
+                "multiqc_snpeff.txt:md5,03a2b1c461cb6e5cccac64033a2f6526",
+                "snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
+                "snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
+                "snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
+                "vep-general-stats.txt:md5,57563be109a57f6edfa427b2b2c310ba",
+                "vep.txt:md5,bf54f689bb0ccab5e1566e48373f768c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T09:56:59.385257"
+    }
+}
diff --git a/tests/annotation_snpeff.nf.test b/tests/annotation_snpeff.nf.test
index 490c2efea4..9addb8f1d7 100644
--- a/tests/annotation_snpeff.nf.test
+++ b/tests/annotation_snpeff.nf.test
@@ -39,40 +39,6 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --tools snpeff") {
-
-        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'
-                snpeff_cache = 's3://annotation-cache/snpeff_cache/'
-                tools = 'snpeff'
-            }
-        }
-
-        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() }
-            )
-        }
-    }
-
     test("Fails with profile test | --tools snpeff --snpeff_db na --build_only_index") {
         when {
             params {
diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap
index 84a9016c92..012faa171c 100644
--- a/tests/annotation_snpeff.nf.test.snap
+++ b/tests/annotation_snpeff.nf.test.snap
@@ -96,8 +96,6 @@
                 "snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
                 "snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
                 "snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
-                "snpEff_summary.html:md5,b0658aa728db5acfb5fae433d411f06a",
-                "test_snpEff.csv:md5,d6ca9f83555aa18445d565692b5ee8c2",
                 "test_snpEff.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a"
             ]
         ],
@@ -105,93 +103,6 @@
             "nf-test": "0.9.1",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-29T09:02:01.062023"
-    },
-    "Run with profile test | --tools snpeff": {
-        "content": [
-            3,
-            {
-                "SNPEFF_SNPEFF": {
-                    "snpeff": "5.1d"
-                },
-                "TABIX_BGZIPTABIX": {
-                    "tabix": 1.2
-                },
-                "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
-                }
-            },
-            [
-                "annotation",
-                "annotation/test",
-                "annotation/test/test_snpEff.ann.vcf.gz",
-                "annotation/test/test_snpEff.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_general_stats.txt",
-                "multiqc/multiqc_data/multiqc_snpeff.txt",
-                "multiqc/multiqc_data/multiqc_software_versions.txt",
-                "multiqc/multiqc_data/multiqc_sources.txt",
-                "multiqc/multiqc_data/snpeff_effects.txt",
-                "multiqc/multiqc_data/snpeff_qualities.txt",
-                "multiqc/multiqc_data/snpeff_variant_effects_region.txt",
-                "multiqc/multiqc_plots",
-                "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_effects-cnt.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_effects-pct.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_qualities.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-cnt.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-log.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct-log.pdf",
-                "multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct.pdf",
-                "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
-                "multiqc/multiqc_plots/png/snpeff_effects-cnt.png",
-                "multiqc/multiqc_plots/png/snpeff_effects-pct.png",
-                "multiqc/multiqc_plots/png/snpeff_qualities.png",
-                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-cnt.png",
-                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-log.png",
-                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct-log.png",
-                "multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct.png",
-                "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
-                "multiqc/multiqc_plots/svg/snpeff_effects-cnt.svg",
-                "multiqc/multiqc_plots/svg/snpeff_effects-pct.svg",
-                "multiqc/multiqc_plots/svg/snpeff_qualities.svg",
-                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-cnt.svg",
-                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-log.svg",
-                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct-log.svg",
-                "multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct.svg",
-                "multiqc/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
-                "reports",
-                "reports/snpeff",
-                "reports/snpeff/test",
-                "reports/snpeff/test/snpEff_summary.html",
-                "reports/snpeff/test/test_snpEff.csv",
-                "reports/snpeff/test/test_snpEff.genes.txt"
-            ],
-            [
-                "multiqc_citations.txt:md5,47e39f5f5f05da6bc38d13aa81fe8b6e",
-                "multiqc_snpeff.txt:md5,03a2b1c461cb6e5cccac64033a2f6526",
-                "snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
-                "snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
-                "snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
-                "snpEff_summary.html:md5,990f2f24d5f37d177bca479706135be7",
-                "test_snpEff.csv:md5,f077b95576c7d137a2fd1d096aa5434c",
-                "test_snpEff.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-10-29T09:04:02.127501"
+        "timestamp": "2024-10-29T10:16:00.665699"
     }
 }
\ No newline at end of file
diff --git a/tests/annotation_vep.nf.test b/tests/annotation_vep.nf.test
index d2ec6ab55c..80659a41b7 100644
--- a/tests/annotation_vep.nf.test
+++ b/tests/annotation_vep.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --tools vep --download_cache") {
+    test("Run with profile test | --tools vep --download_cache --vep_include_fasta") {
 
         when {
             params {
@@ -39,40 +39,6 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --tools vep --vep_include_fasta") {
-
-        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'
-                vep_cache = 's3://annotation-cache/vep_cache/'
-                tools = 'vep'
-            }
-        }
-
-        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() }
-            )
-        }
-    }
-
     test("Fails with profile test | --tools vep --vep_cache_version 1 --build_only_index") {
         when {
             params {
diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap
index 300780733f..dd13a715dc 100644
--- a/tests/annotation_vep.nf.test.snap
+++ b/tests/annotation_vep.nf.test.snap
@@ -1,61 +1,5 @@
 {
-    "Run with profile test | --tools vep --vep_include_fasta": {
-        "content": [
-            3,
-            {
-                "ENSEMBLVEP_VEP": {
-                    "ensemblvep": 113.0
-                },
-                "TABIX_TABIX": {
-                    "tabix": 1.2
-                },
-                "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
-                }
-            },
-            [
-                "annotation",
-                "annotation/test",
-                "annotation/test/test_VEP.ann.vcf.gz",
-                "annotation/test/test_VEP.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_data/vep-general-stats.txt",
-                "multiqc/multiqc_data/vep.txt",
-                "multiqc/multiqc_plots",
-                "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/vep-general-stats.pdf",
-                "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/vep-general-stats.png",
-                "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/vep-general-stats.svg",
-                "multiqc/multiqc_report.html",
-                "pipeline_info",
-                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
-                "reports",
-                "reports/EnsemblVEP",
-                "reports/EnsemblVEP/test",
-                "reports/EnsemblVEP/test/test_VEP.ann.summary.html"
-            ],
-            [
-                "multiqc_citations.txt:md5,afe6b13a9c0770828d9bc9515d6db802",
-                "vep-general-stats.txt:md5,2fca07ac5623e758cac3ce49d9f6e3b0",
-                "vep.txt:md5,60a5d57c60308aba2aa6206f903d27e9"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-24T11:49:16.737881"
-    },
-    "Run with profile test | --tools vep --download_cache": {
+    "Run with profile test | --tools vep --download_cache --vep_include_fasta": {
         "content": [
             4,
             {
@@ -331,9 +275,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-23T15:00:39.082074"
+        "timestamp": "2024-10-29T10:19:17.846465"
     }
 }
\ No newline at end of file
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index d7fd79258e..a691b4019b 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -439,20 +439,6 @@ tiddit:
   - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_tiddit.yml
 
-# annotate
-
-## merge
-merge:
-  - conf/modules/annotate.config
-  - modules/nf-core/ensemblvep/vep/**
-  - modules/nf-core/snpeff/snpeff/**
-  - modules/nf-core/tabix/bgziptabix/**
-  - subworkflows/local/vcf_annotate_all/**
-  - subworkflows/nf-core/vcf_annotate_ensemblvep/**
-  - subworkflows/nf-core/vcf_annotate_snpeff/**
-  - tests/csv/3.0/vcf_single.csv
-  - tests/test_annotation_merge.yml
-
 # postprocessing
 
 ## concatenate germline vcfs
diff --git a/tests/test_annotation_merge.yml b/tests/test_annotation_merge.yml
deleted file mode 100644
index 03b163a1af..0000000000
--- a/tests/test_annotation_merge.yml
+++ /dev/null
@@ -1,58 +0,0 @@
-- name: Run snpEff followed by VEP
-  command: nextflow run main.nf -profile test,annotation --tools merge --outdir results --download_cache
-  tags:
-    - annotation
-    - merge
-  files:
-    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.ann.summary.html
-      contains: ["test_snpEff.ann.vcf.gz</pre></td></tr><tr><td>Output file</td><td><pre>test_snpEff_VEP.ann.vcf.gz"]
-    - path: results/multiqc
-    - path: results/annotation/test/test_snpEff.ann.vcf.gz
-      should_exist: false
-    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
-      should_exist: false
-    - path: results/annotation/test/test_VEP.ann.vcf.gz
-      should_exist: false
-    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
-      should_exist: false
-    - path: results/reports/snpeff/test/snpEff_summary.html
-      should_exist: false
-    - path: results/reports/snpeff/test/test_snpEff.csv
-      should_exist: false
-    - path: results/reports/snpeff/test/test_snpEff.genes.txt
-      should_exist: false
-    - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
-      should_exist: false
-- name: Run VEP and snpEff followed by VEP
-  command: nextflow run main.nf -profile test,annotation --tools merge,snpeff,vep --outdir results --download_cache
-  tags:
-    - annotation
-    - merge
-  files:
-    - path: results/annotation/test/test_VEP.ann.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_snpEff.ann.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
-    # binary changes md5sums on reruns
-    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
-    # binary changes md5sums on reruns
-    - path: results/multiqc
-    - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
-    # text-based file changes md5sums on reruns
-    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.ann.summary.html
-    # text-based file changes md5sums on reruns
-    - path: results/reports/snpeff/test/snpEff_summary.html
-    # text-based file changes md5sums on reruns
-    - path: results/reports/snpeff/test/test_snpEff.csv
-    # text-based file changes md5sums on reruns
-    - path: results/reports/snpeff/test/test_snpEff.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a