add merge + refactor snpeff/vep

nf-core · Oct 29, 2024 · 565ef20 · 565ef20
1 parent cb85367
commit 565ef20
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Showing 9 changed files with 290 additions and 291 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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 {