$ nf-test test modules/local/virjendb/prepareupdate/ --profile docker 🚀 nf-test 0.9.2 https://www.nf-test.com (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr Warning: This pipeline has no nf-test config file. Test Process VIRJENDB_PREPAREUPDATE Test [7b2dd1d5] 'vjndb update test - fna' java.lang.RuntimeException: Different Snapshot: --- /tmp/expected10923945915938493867js +++ /tmp/found493571077519850827json on @@ -1,13 @@ @@ +1,30 @@ 1 [ 1 [ 2 { 2 { + 3 "0": [ + 4 "combined_for_vclust.f na.gz:md5,f166074cd9a9b7341376d5a0fff5c eee" + 5 ], + 6 "1": [ + 7 "new_hashed_reps.csv:m d5,662f4ab26a0711a5d709b478c6b8cb15" + 8 ], + 9 "2": [ + 10 [ + 11 "VIRJENDB_PREPAREU PDATE", + 12 "biopython", + 13 "1.87" + 14 ] + 15 ], 3 "combined_reps_fna": [ 16 "combined_reps_fna": [ ! 4 ! 17 "combined_for_vclust.f na.gz:md5,f166074cd9a9b7341376d5a0fff5c eee" 5 ], 18 ], 6 "hashed_reps": [ 19 "hashed_reps": [ ! 7 ! 20 "new_hashed_reps.csv:m d5,662f4ab26a0711a5d709b478c6b8cb15" 8 ], 21 ], 9 "versions_biopython": [ 22 "versions_biopython": [ ! 10 ! 23 [ + 24 "VIRJENDB_PREPAREU PDATE", + 25 "biopython", + 26 "1.87" + 27 ] 11 ] 28 ] 12 } 29 } 13 ] 30 ] java.lang.RuntimeException: A snapshot with id 'vjndb update test - fna' already exists. Snapshot ids have to be unique, and a test can only have one unnamed snapshot. FAILED (7.523s) Assertion failed: 2 of 3 assertions failed Nextflow stdout: Nextflow stderr: Nextflow 26.04.1 is available - Please consider updating your version to it Test [22b1fce9] 'vjndb update test - fna - stub' java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:294) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:284) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:196) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:81) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:112) at com.askimed.nf.test.util.FileUtil.getMd5(FileUtil.java:103) at com.askimed.nf.test.lang.extensions.PathExtension.getMd5(PathExtension.java:21) at com.askimed.nf.test.lang.extensions.util.PathConverter.serializeFile(PathConverter.java:57) at com.askimed.nf.test.lang.extensions.util.PathConverter.convert(PathConverter.java:42) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:185) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:202) at groovy.json.DefaultJsonGenerator.writeMapEntry(DefaultJsonGenerator.java:381) at groovy.json.DefaultJsonGenerator.writeMap(DefaultJsonGenerator.java:369) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:200) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeArray(DefaultJsonGenerator.java:279) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:221) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.toJson(DefaultJsonGenerator.java:98) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.toString(SnapshotFileItem.java:80) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.equals(SnapshotFileItem.java:64) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:57) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:27) at com.askimed.nf.test.lang.extensions.Snapshot$match.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test:53) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:39) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test:50) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:298) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at com.askimed.nf.test.App.run(App.java:39) at com.askimed.nf.test.App.main(App.java:46) java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:294) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:284) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:196) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:81) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:112) at com.askimed.nf.test.util.FileUtil.getMd5(FileUtil.java:103) at com.askimed.nf.test.lang.extensions.PathExtension.getMd5(PathExtension.java:21) at com.askimed.nf.test.lang.extensions.util.PathConverter.serializeFile(PathConverter.java:57) at com.askimed.nf.test.lang.extensions.util.PathConverter.convert(PathConverter.java:42) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:185) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:202) at groovy.json.DefaultJsonGenerator.writeMapEntry(DefaultJsonGenerator.java:381) at groovy.json.DefaultJsonGenerator.writeMap(DefaultJsonGenerator.java:369) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:200) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeArray(DefaultJsonGenerator.java:279) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:221) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.toJson(DefaultJsonGenerator.java:98) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.toString(SnapshotFileItem.java:80) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.equals(SnapshotFileItem.java:64) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:57) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:27) at com.askimed.nf.test.lang.extensions.Snapshot$match.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test:53) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:39) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test:50) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:298) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at com.askimed.nf.test.App.run(App.java:39) at com.askimed.nf.test.App.main(App.java:46) java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:294) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:284) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:196) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:81) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:112) at com.askimed.nf.test.util.FileUtil.getMd5(FileUtil.java:103) at com.askimed.nf.test.lang.extensions.PathExtension.getMd5(PathExtension.java:21) at com.askimed.nf.test.lang.extensions.util.PathConverter.serializeFile(PathConverter.java:57) at com.askimed.nf.test.lang.extensions.util.PathConverter.convert(PathConverter.java:42) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:185) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:202) at groovy.json.DefaultJsonGenerator.writeMapEntry(DefaultJsonGenerator.java:381) at groovy.json.DefaultJsonGenerator.writeMap(DefaultJsonGenerator.java:369) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:200) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeArray(DefaultJsonGenerator.java:279) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:221) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.toJson(DefaultJsonGenerator.java:98) at com.askimed.nf.test.lang.extensions.util.SnapshotDiffUtil.writeSnapshotToFile(SnapshotDiffUtil.java:95) at com.askimed.nf.test.lang.extensions.util.SnapshotDiffUtil.getDiff(SnapshotDiffUtil.java:37) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.equals(SnapshotFileItem.java:69) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:57) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:27) at com.askimed.nf.test.lang.extensions.Snapshot$match.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test:53) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:39) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test:50) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:298) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at com.askimed.nf.test.App.run(App.java:39) at com.askimed.nf.test.App.main(App.java:46) java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:294) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:284) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:196) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:81) at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:112) at com.askimed.nf.test.util.FileUtil.getMd5(FileUtil.java:103) at com.askimed.nf.test.lang.extensions.PathExtension.getMd5(PathExtension.java:21) at com.askimed.nf.test.lang.extensions.util.PathConverter.serializeFile(PathConverter.java:57) at com.askimed.nf.test.lang.extensions.util.PathConverter.convert(PathConverter.java:42) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:185) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:202) at groovy.json.DefaultJsonGenerator.writeMapEntry(DefaultJsonGenerator.java:381) at groovy.json.DefaultJsonGenerator.writeMap(DefaultJsonGenerator.java:369) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:200) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.writeIterator(DefaultJsonGenerator.java:396) at groovy.json.DefaultJsonGenerator.writeArray(DefaultJsonGenerator.java:279) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:221) at groovy.json.DefaultJsonGenerator.writeObject(DefaultJsonGenerator.java:164) at groovy.json.DefaultJsonGenerator.toJson(DefaultJsonGenerator.java:98) at com.askimed.nf.test.lang.extensions.util.SnapshotDiffUtil.writeSnapshotToFile(SnapshotDiffUtil.java:95) at com.askimed.nf.test.lang.extensions.util.SnapshotDiffUtil.getDiff(SnapshotDiffUtil.java:37) at com.askimed.nf.test.lang.extensions.SnapshotFileItem.equals(SnapshotFileItem.java:69) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:57) at com.askimed.nf.test.lang.extensions.Snapshot.match(Snapshot.java:27) at com.askimed.nf.test.lang.extensions.Snapshot$match.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test:53) at main_nf$_run_closure1$_closure3$_closure12$_closure15.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:39) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test:50) at main_nf$_run_closure1$_closure3$_closure12.doCall(main.nf.test) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) at groovy.lang.Closure.call(Closure.java:427) at groovy.lang.Closure.call(Closure.java:406) at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:298) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at com.askimed.nf.test.App.run(App.java:39) at com.askimed.nf.test.App.main(App.java:46) java.lang.RuntimeException: Different Snapshot: --- /tmp/expected8326996663113188315jso +++ /tmp/found12862293680527242529json n @@ -1,7 @@ @@ +1,20 @@ 1 [ 1 [ 2 { 2 { + 3 "0": [ + 4 "/home/uridavid/Code/v jdb-clustering/.nf-test/tests/22b1fce91 07d1a6cd3cc30f81525d4b/work/04/ef94a4c7 b3a13399b506280b8b90ec/combined_for_vcl ust.fna.gz" + 5 ], + 6 "1": [ + 7 "new_hashed_reps.csv:m d5,d41d8cd98f00b204e9800998ecf8427e" + 8 ], + 9 "2": [ + 10 [ + 11 "VIRJENDB_PREPAREU PDATE", + 12 "biopython", + 13 "1.87" + 14 ] + 15 ], 3 "combined_reps_fna": [ 16 "combined_reps_fna": [ ! 4 "/home/uridavid/Code/v ! 17 "/home/uridavid/Code/v jdb-clustering/.nf-test/tests/22b1fce91 jdb-clustering/.nf-test/tests/22b1fce91 07d1a6cd3cc30f81525d4b/work/eb/2533a63e 07d1a6cd3cc30f81525d4b/work/04/ef94a4c7 4d5399b06d77aa5762f809/combined_for_vcl b3a13399b506280b8b90ec/combined_for_vcl ust.fna.gz" ust.fna.gz" 5 ], 18 ], 6 "hashed_reps": [ 19 "hashed_reps": [ 7 "new_hashed_reps.csv:m 20 "new_hashed_reps.csv:m d5,d41d8cd98f00b204e9800998ecf8427e" d5,d41d8cd98f00b204e9800998ecf8427e" @@ -10,7 @@ @@ +23,7 @@ 10 [ 23 [ 11 "VIRJENDB_PREPAREU 24 "VIRJENDB_PREPAREU PDATE", PDATE", 12 "biopython", 25 "biopython", ! 13 "1.81" ! 26 "1.87" 14 ] 27 ] 15 ] 28 ] 16 } 29 } FAILED (7.57s) Assertion failed: 1 of 2 assertions failed Nextflow stdout: Nextflow stderr: Nextflow 26.04.1 is available - Please consider updating your version to it Obsolete snapshots can only be checked if all tests of a file are executed successful. FAILURE: Executed 2 tests in 15.131s (2 failed)