-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy path.nf-test.log
More file actions
85 lines (85 loc) · 15.2 KB
/
Copy path.nf-test.log
File metadata and controls
85 lines (85 loc) · 15.2 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
Nov-05 13:11:07.354 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2
Nov-05 13:11:07.382 [main] INFO com.askimed.nf.test.App - Arguments: [test, ., --update-snapshot]
Nov-05 13:11:08.534 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.04.7
Nov-05 13:11:08.537 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /Users/tylergross/Desktop/samplesheet_generator_pdmr/nf-test.config...
Nov-05 13:11:09.089 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 35 files from directory /Users/tylergross/Desktop/samplesheet_generator_pdmr in 0.065 sec
Nov-05 13:11:09.091 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 12 files containing tests.
Nov-05 13:11:09.092 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/hlatyping.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/xengsort.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/data_download.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/db_merge.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/rna_seq.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/main.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/purecn.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/final_merge.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/epitope.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/vcf_expression_annotator.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/sarek.nf.test, /Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/neo_downstream.nf.test]
Nov-05 13:11:09.703 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 14 tests to execute.
Nov-05 13:11:09.704 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
Nov-05 13:11:09.704 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/main.nf.test'.
Nov-05 13:11:09.705 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'fe46811f: Should run without failures'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
Nov-05 13:11:18.780 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'fe46811f: Should run without failures' finished. status: PASSED
Nov-05 13:11:18.784 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: false, skipped tests: false, failed tests: false
Nov-05 13:11:18.784 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process DATA_DOWNLOAD' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/data_download.nf.test'.
Nov-05 13:11:18.784 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'd4712d60: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:25.611 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/data_download.nf.test.snap'
Nov-05 13:11:25.625 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:25.625 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'd4712d60: Should run without failures' finished. status: PASSED
Nov-05 13:11:25.625 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '1792074a: Should run in stub mode and check URLs'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:30.740 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '1792074a: Should run in stub mode and check URLs' finished. status: PASSED
Nov-05 13:11:30.741 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process DATA_DOWNLOAD' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:30.741 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process DB_MERGE' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/db_merge.nf.test'.
Nov-05 13:11:30.741 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2ea587e5: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:35.768 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/db_merge.nf.test.snap'
Nov-05 13:11:35.771 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:35.771 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2ea587e5: Should run without failures' finished. status: PASSED
Nov-05 13:11:35.771 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process DB_MERGE' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:35.772 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process EPITOPE' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/epitope.nf.test'.
Nov-05 13:11:35.772 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '66393a0a: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:40.583 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/epitope.nf.test.snap'
Nov-05 13:11:40.585 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:40.585 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '66393a0a: Should run without failures' finished. status: PASSED
Nov-05 13:11:40.586 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process EPITOPE' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:40.586 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process FINAL_MERGE' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/final_merge.nf.test'.
Nov-05 13:11:40.586 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'ae9b4c56: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:45.544 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/final_merge.nf.test.snap'
Nov-05 13:11:45.545 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:45.545 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'ae9b4c56: Should run without failures' finished. status: PASSED
Nov-05 13:11:45.545 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process FINAL_MERGE' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:45.546 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process HLATYPING' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/hlatyping.nf.test'.
Nov-05 13:11:45.546 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '967c48b1: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:50.708 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/hlatyping.nf.test.snap'
Nov-05 13:11:50.711 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:50.711 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '967c48b1: Should run without failures' finished. status: PASSED
Nov-05 13:11:50.711 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process HLATYPING' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:50.711 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process NEO_DOWNSTREAM' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/neo_downstream.nf.test'.
Nov-05 13:11:50.711 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d5fd2b2: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:11:55.884 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/neo_downstream.nf.test.snap'
Nov-05 13:11:55.885 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:11:55.885 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d5fd2b2: Should run without failures' finished. status: PASSED
Nov-05 13:11:55.885 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process NEO_DOWNSTREAM' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:11:55.885 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process PURECN' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/purecn.nf.test'.
Nov-05 13:11:55.885 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'bedccaaa: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:00.870 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/purecn.nf.test.snap'
Nov-05 13:12:00.870 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:12:00.870 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'bedccaaa: Should run without failures' finished. status: PASSED
Nov-05 13:12:00.871 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process PURECN' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:12:00.871 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process RNA_SEQ' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/rna_seq.nf.test'.
Nov-05 13:12:00.871 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'f11e02e6: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:06.126 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/rna_seq.nf.test.snap'
Nov-05 13:12:06.127 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:12:06.127 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'f11e02e6: Should run without failures' finished. status: PASSED
Nov-05 13:12:06.127 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process RNA_SEQ' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:12:06.128 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process SAREK' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/sarek.nf.test'.
Nov-05 13:12:06.128 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '51a2259a: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:11.141 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/sarek.nf.test.snap'
Nov-05 13:12:11.143 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:12:11.143 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '51a2259a: Should run without failures' finished. status: PASSED
Nov-05 13:12:11.143 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process SAREK' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:12:11.143 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process VCF_EXPRESSION_ANNOTATOR' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/vcf_expression_annotator.nf.test'.
Nov-05 13:12:11.144 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'bdf3a0ba: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:15.962 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/vcf_expression_annotator.nf.test.snap'
Nov-05 13:12:15.964 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:12:15.964 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'bdf3a0ba: Should run without failures' finished. status: PASSED
Nov-05 13:12:15.965 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process VCF_EXPRESSION_ANNOTATOR' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:12:15.965 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process XENGSORT' from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/xengsort.nf.test'.
Nov-05 13:12:15.965 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'ed3ee71d: Should run without failures'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:21.051 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/Users/tylergross/Desktop/samplesheet_generator_pdmr/tests/modules/xengsort.nf.test.snap'
Nov-05 13:12:21.053 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures' match.
Nov-05 13:12:21.053 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'ed3ee71d: Should run without failures' finished. status: PASSED
Nov-05 13:12:21.053 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'ae998218: Should run without failures in RNA-only mode'. type: com.askimed.nf.test.lang.process.ProcessTest
Nov-05 13:12:26.147 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'Should run without failures in RNA-only mode' match.
Nov-05 13:12:26.147 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'ae998218: Should run without failures in RNA-only mode' finished. status: PASSED
Nov-05 13:12:26.147 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process XENGSORT' finished. snapshot file: true, skipped tests: false, failed tests: false
Nov-05 13:12:26.147 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 14 tests. 0 tests failed. Done!