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nourmahfelnourmahfel
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Fix tests
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‎.nf-test.log‎

Lines changed: 18 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
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Mar-23 21:09:20.741 [main] INFO com.askimed.nf.test.App - nf-test 0.9.4
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Mar-23 21:09:20.752 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test]
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Mar-23 21:09:21.729 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.10.4
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Mar-23 21:09:21.731 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/nmahfel/nf-training/longraredisease/nf-test.config...
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Mar-23 21:09:22.567 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 108 files from directory /home/nmahfel/nf-training/longraredisease in 0.252 sec
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Mar-23 21:09:22.568 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
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Mar-23 21:09:22.568 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/home/nmahfel/nf-training/longraredisease/tests/default.nf.test]
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Mar-23 21:09:22.695 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
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Mar-23 21:09:22.696 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
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Mar-23 21:09:22.696 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test'.
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Mar-23 21:09:22.696 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '87a975d0: Longraredisease full test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
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Mar-23 21:16:52.049 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '87a975d0: Longraredisease full test' finished. status: PASSED
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Mar-23 21:16:52.052 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: false, skipped tests: false, failed tests: false
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Mar-23 21:16:52.052 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!
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Mar-24 08:55:06.510 [main] INFO com.askimed.nf.test.App - nf-test 0.9.4
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Mar-24 08:55:06.521 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test]
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Mar-24 08:55:07.287 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.10.4
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Mar-24 08:55:07.288 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/nmahfel/nf-training/longraredisease/nf-test.config...
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Mar-24 08:55:08.996 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 109 files from directory /home/nmahfel/nf-training/longraredisease in 0.122 sec
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Mar-24 08:55:08.997 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
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Mar-24 08:55:08.997 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/home/nmahfel/nf-training/longraredisease/tests/default.nf.test]
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Mar-24 08:55:09.193 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
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Mar-24 08:55:09.194 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
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Mar-24 08:55:09.194 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test pipeline' from file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test'.
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Mar-24 08:55:09.194 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '461a1912: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
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Mar-24 09:02:14.597 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Init new snapshot file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test.snap'
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Mar-24 09:02:14.600 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshot '-profile test' not found.
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Mar-24 09:02:14.600 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Created snapshot '-profile test'
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Mar-24 09:02:23.879 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test.snap'
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Mar-24 09:02:23.880 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '461a1912: -profile test' finished. status: PASSED
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Mar-24 09:02:23.882 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: true, skipped tests: false, failed tests: false
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Mar-24 09:02:23.883 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

‎conf/test.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ params {
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sv = true // Enable structural variant calling
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merge_sv = true
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snv = true // Enable SNV calling
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cnv = false // Enable CNV calling with HiFiCNV if cnv_spectre is false
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cnv = false // Enable CNV calling - spectre for ont and hificnv for pacbio
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str = true // Enable STR analysis
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qc = true // Enable quality control
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methyl = true // Enable methylation calling

‎nextflow.config‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,14 +12,14 @@ params {
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use_winnowmap = false
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winnowmap_model = null
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haplotag_bam = true
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trio_analysis = true
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trio_analysis = false
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filter_targets = false
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targets_bed = null
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generate_bam_stats = true
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generate_coverage_report = true
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sv = true
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snv = true
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cnv = true
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cnv = false
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str = true
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qc = true
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methyl = true

‎nextflow_schema.json‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -87,7 +87,7 @@
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},
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"trio_analysis": {
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"type": "boolean",
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"default": true,
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"default": false,
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"description": "Enable trio analysis for SNV calling and phasing.",
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"fa_icon": "fas fa-users"
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},
@@ -129,7 +129,7 @@
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},
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"cnv": {
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"type": "boolean",
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"default": true,
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"default": false,
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"description": "Enable CNV calling with HiFiCNV if cnv_spectre is false.",
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"fa_icon": "fas fa-chart-area"
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},

‎tests/default.nf.test‎

Lines changed: 15 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -14,14 +14,20 @@ nextflow_pipeline {
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}
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then {
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// Basic success check
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assert workflow.success
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// Check output directory exists
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assert path("$outputDir").exists()
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// Check pipeline info directory exists
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assert path("$outputDir/pipeline_info").exists()
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}
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
22+
{ assert workflow.success},
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{ assert snapshot(
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
25+
removeNextflowVersion("$outputDir/pipeline_info/nf_core_longraredisease_software_mqc_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() })
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}
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}
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}

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