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Dec-16 02:15:48.643 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2 | ||
Dec-16 02:15:48.667 [main] INFO com.askimed.nf.test.App - Arguments: [test, --update-snapshot, --wipe-snapshot, --profile, +docker, workflows/tests/aligner/bowtie2.nf.test, workflows/tests/aligner/bwamem2.nf.test, workflows/tests/aligner/bwa.nf.test, workflows/tests/aligner/dragmap.nf.test, workflows/tests/aligner/hisat2.nf.test, workflows/tests/aligner/star.nf.test] | ||
Dec-16 02:15:49.565 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.2 | ||
Dec-16 02:15:49.566 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /workspace/nascent/nf-test.config... | ||
Dec-16 02:15:50.382 [main] WARN com.askimed.nf.test.nextflow.NextflowScript - Module /workspace/nascent/subworkflows/local/dreg_prep/main.nf: Dependency '/workspace/nascent/subworkflows/local/dreg_prep/../modules/nf-core/bedtools/bamtobed/main.nf' not found. | ||
Dec-16 02:15:50.412 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 230 files from directory /workspace/nascent in 0.386 sec | ||
Dec-16 02:15:50.415 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 6 files containing tests. | ||
Dec-16 02:15:50.415 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/workspace/nascent/workflows/tests/aligner/dragmap.nf.test, /workspace/nascent/workflows/tests/aligner/bwa.nf.test, /workspace/nascent/workflows/tests/aligner/star.nf.test, /workspace/nascent/workflows/tests/aligner/bowtie2.nf.test, /workspace/nascent/workflows/tests/aligner/hisat2.nf.test, /workspace/nascent/workflows/tests/aligner/bwamem2.nf.test] | ||
Dec-16 02:15:51.025 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 9 tests to execute. | ||
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan | ||
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Bowtie2' from file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test'. | ||
Dec-16 02:15:51.026 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e3410fa6: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:18:37.490 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap' | ||
Dec-16 02:18:37.673 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:18:37.673 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:18:37.748 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap' | ||
Dec-16 02:18:37.749 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e3410fa6: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:18:37.752 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:18:37.809 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bowtie2.nf.test.snap' | ||
Dec-16 02:18:37.809 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Bowtie2' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:18:37.812 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'BWA' from file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test'. | ||
Dec-16 02:18:37.812 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e912cd0f: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:22:23.045 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap' | ||
Dec-16 02:22:23.366 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:22:23.367 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:22:23.501 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap' | ||
Dec-16 02:22:23.501 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e912cd0f: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:22:23.502 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'ca549b93: Should work with BWA Index'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:24:03.940 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should work with BWA Index' match. | ||
Dec-16 02:24:03.940 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'ca549b93: Should work with BWA Index' finished. status: PASSED | ||
Dec-16 02:24:03.941 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '71a06a5b: Should work with gzipped references'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:25:20.210 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should work with gzipped references' match. | ||
Dec-16 02:25:20.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '71a06a5b: Should work with gzipped references' finished. status: PASSED | ||
Dec-16 02:25:20.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:25:20.664 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwa.nf.test.snap' | ||
Dec-16 02:25:20.664 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'BWA' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:25:20.666 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'bwamem2' from file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test'. | ||
Dec-16 02:25:20.666 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '40528c2d: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:27:44.578 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap' | ||
Dec-16 02:27:44.713 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:27:44.713 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:27:44.920 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap' | ||
Dec-16 02:27:44.920 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '40528c2d: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:27:44.921 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:27:45.186 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/bwamem2.nf.test.snap' | ||
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'bwamem2' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'DRAGMAP' from file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test'. | ||
Dec-16 02:27:45.186 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'e16b50e4: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:31:00.293 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap' | ||
Dec-16 02:31:00.427 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:31:00.428 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:31:00.502 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap' | ||
Dec-16 02:31:00.502 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'e16b50e4: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:31:00.503 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:31:00.610 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/dragmap.nf.test.snap' | ||
Dec-16 02:31:00.610 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'DRAGMAP' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:31:00.611 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'HISAT2' from file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test'. | ||
Dec-16 02:31:00.611 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '54f5dffc: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:34:03.031 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap' | ||
Dec-16 02:34:03.729 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:34:03.729 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:34:04.295 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap' | ||
Dec-16 02:34:04.296 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '54f5dffc: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:34:04.296 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:34:04.846 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/hisat2.nf.test.snap' | ||
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'HISAT2' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'STAR' from file '/workspace/nascent/workflows/tests/aligner/star.nf.test'. | ||
Dec-16 02:34:04.846 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '32b4754c: Should run with defaults'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:38:34.918 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap' | ||
Dec-16 02:38:39.215 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with defaults' do not match. Update snapshots flag set. | ||
Dec-16 02:38:39.216 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'Should run with defaults' | ||
Dec-16 02:38:42.370 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap' | ||
Dec-16 02:38:42.370 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '32b4754c: Should run with defaults' finished. status: PASSED | ||
Dec-16 02:38:42.370 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '99482460: Should run with gzipped gtf'. type: com.askimed.nf.test.lang.pipeline.PipelineTest | ||
Dec-16 02:42:52.588 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'gzip_software_versions' match. | ||
Dec-16 02:42:52.589 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run with gzipped gtf' match. | ||
Dec-16 02:42:52.589 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '99482460: Should run with gzipped gtf' finished. status: PASSED | ||
Dec-16 02:42:52.590 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Clean up obsolete snapshots | ||
Dec-16 02:42:57.042 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/workspace/nascent/workflows/tests/aligner/star.nf.test.snap' | ||
Dec-16 02:42:57.042 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'STAR' finished. snapshot file: true, skipped tests: false, failed tests: false | ||
Dec-16 02:42:57.043 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 9 tests. 0 tests failed. Done! |
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