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Fix tests
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‎.nf-test.log‎

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Mar-24 16:59:48.775 [main] INFO com.askimed.nf.test.App - nf-test 0.9.4
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Mar-24 16:59:48.787 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test, --profile, docker, --verbose]
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Mar-24 16:59:49.608 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.10.4
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Mar-24 16:59:49.610 [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 16:59:50.322 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 110 files from directory /home/nmahfel/nf-training/longraredisease in 0.092 sec
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Mar-24 16:59:50.323 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
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Mar-24 16:59:50.323 [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 16:59:50.554 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
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Mar-24 16:59:50.554 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
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Mar-24 16:59:50.554 [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 16:59:50.555 [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 17:07:58.605 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '461a1912: -profile test' finished. status: FAILED
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org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 1 of 2 assertions failed
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at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:47)
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at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
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at default_nf$_run_closure1$_closure2$_closure4.doCall(default.nf.test:21)
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at default_nf$_run_closure1$_closure2$_closure4.doCall(default.nf.test)
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at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
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at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
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at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
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at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
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at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1009)
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at groovy.lang.Closure.call(Closure.java:433)
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at groovy.lang.Closure.call(Closure.java:412)
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at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
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at com.askimed.nf.test.lang.pipeline.PipelineTest.execute(PipelineTest.java:135)
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at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:172)
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at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:322)
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at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
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at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
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at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
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at picocli.CommandLine.access$1300(CommandLine.java:145)
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at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
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at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
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at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
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at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
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at picocli.CommandLine.execute(CommandLine.java:2078)
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at com.askimed.nf.test.App.run(App.java:39)
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at com.askimed.nf.test.App.main(App.java:46)
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Mar-24 17:07:58.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: false, skipped tests: false, failed tests: true
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Mar-24 17:07:58.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 1 tests failed. Done!
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Mar-24 17:25:03.915 [main] INFO com.askimed.nf.test.App - nf-test 0.9.4
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Mar-24 17:25:03.931 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/default.nf.test, --update-snapshot]
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Mar-24 17:25:04.849 [main] INFO com.askimed.nf.test.App - Nextflow Version: 25.10.4
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Mar-24 17:25:04.850 [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 17:25:05.669 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 110 files from directory /home/nmahfel/nf-training/longraredisease in 0.191 sec
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Mar-24 17:25:05.671 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
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Mar-24 17:25:05.671 [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 17:25:05.909 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
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Mar-24 17:25:05.910 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
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Mar-24 17:25:05.910 [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 17:25:05.911 [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 17:31:45.749 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/nmahfel/nf-training/longraredisease/tests/default.nf.test.snap'
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Mar-24 17:31:45.761 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots '-profile test' do not match. Update snapshots flag set.
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Mar-24 17:31:45.762 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot '-profile test'
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Mar-24 17:31:45.764 [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 17:31:45.765 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '461a1912: -profile test' finished. status: PASSED
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Mar-24 17:31:45.767 [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 17:31:45.769 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

‎README.md‎

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[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.6-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
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[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/longraredisease)

‎tests/default.nf.test.snap‎

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{
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"-profile test": {
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"content": [
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true
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[
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"versions_yml:",
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"nf_core_longraredisease_software_mqc_versions.yml"
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]
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],
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"timestamp": "2026-03-24T16:21:12.978386193",
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"timestamp": "2026-03-24T17:31:45.762014127",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"

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