create tests

nf-test.config

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+config {
+    // location for all nf-tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "conf/test.config"
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+
+    // Include plugins
+    plugins {
+        load "[email protected]"
+        load "[email protected]"
+    }
+}

tests/.nftignore

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+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_general_stats.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/picard_deduplication.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+pipeline_info/*.{html,json,txt,yml}

tests/annotation.nf.test

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+nextflow_pipeline {
+
+    name "Test pipeline | annotation"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_rnavar"
+
+    test("Run with profile test | annotation with snpeff") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                annotate_tools = 'snpeff'
+                download_cache = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | annotation with vep") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                annotate_tools = 'vep'
+                download_cache = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | annotation with merge") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                annotate_tools = 'merge'
+                download_cache = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+}

tests/bam_csi.nf.test

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+nextflow_pipeline {
+
+    name "Test pipeline | bam_csi_index"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_rnavar"
+
+    test("Run with profile test | bam_csi_index") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                bam_csi_index = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+}

tests/default.nf.test

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+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_rnavar"
+
+    test("Run with profile test") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+}

tests/removeduplicates.nf.test

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+nextflow_pipeline {
+
+    name "Test pipeline | remove_duplicates"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_rnavar"
+
+    test("Run with profile test | remove_duplicates") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                remove_duplicates = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+}

tests/skip_baserecalibration.nf.test

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+nextflow_pipeline {
+
+    name "Test pipeline | skip_baserecalibration"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_rnavar"
+
+    test("Run with profile test | skip_baserecalibration") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                skip_baserecalibration = true
+            }
+        }
+
+        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_rnavar_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name
+                ).match() }
+            )
+        }
+    }
+}