Dear
When trying to run the nf-core proteinfold pipeline, I quickly run into the following error before the pipeline starts:
N E X T F L O W ~ version 26.04.6
WARN: This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, but 'nf-core/proteinfold' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command.
Error modules_colabfold.config:40:9: If statements cannot be mixed with config statements
│ 40 | if (params.use_gpu) {
│ | ^^^^^^^^^^^^^^^^^^^^^
│ 41 | accelerator = 1
╰ 42 | }
ERROR ~ Config parsing failed
-- Check '.nextflow.log' file for details
The full log looks as follows:
Aug-31 10:34:11.678 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/proteinfold -profile singularity --input input.csv --outdir proteinfol_results --mode colabfold
Aug-31 10:34:11.776 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 26.04.6
Aug-31 10:34:11.799 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/user/leuven/382/vsc38205/.nextflow/plugins; core-plugins: nf-amazon@3.9.2,nf-azure@1.22.6,nf-cloudcache@0.6.0,nf-codecommit@0.5.3,nf-console@1.3.0,nf-google@1.27.3,nf-k8s@1.5.4,nf-seqera@0.21.1,nf-tower@1.28.2,nf-wave@1.21.0
Aug-31 10:34:11.818 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-31 10:34:11.819 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-31 10:34:11.823 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.14.1 in 'deployment' mode
Aug-31 10:34:11.839 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config
Aug-31 10:34:11.932 [main] DEBUG nextflow.plugin.PluginUpdater - Using plugin repository: HttpPluginRepository [registry]; url=https://registry.nextflow.io/api
Aug-31 10:34:11.938 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-31 10:34:11.949 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /user/leuven/382/vsc38205/.nextflow/scm
Aug-31 10:34:11.975 [main] DEBUG nextflow.scm.AssetManager - Legacy repository detected, selecting legacy strategy
Aug-31 10:34:12.038 [main] DEBUG nextflow.config.ConfigParserFactory - Using config parser v2
Aug-31 10:34:12.713 [main] DEBUG nextflow.scm.AssetManager - Git config: /user/leuven/382/vsc38205/.nextflow/assets/nf-core/proteinfold/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/proteinfold.git
Aug-31 10:34:12.761 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Aug-31 10:34:12.775 [main] DEBUG nextflow.scm.AssetManager - Git config: /user/leuven/382/vsc38205/.nextflow/assets/nf-core/proteinfold/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/proteinfold.git
Aug-31 10:34:12.800 [main] WARN nextflow.cli.CmdRun - This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, but 'nf-core/proteinfold' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command.
Aug-31 10:34:13.546 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /user/leuven/382/vsc38205/.nextflow/assets/nf-core/proteinfold/nextflow.config
Aug-31 10:34:13.548 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /user/leuven/382/vsc38205/.nextflow/assets/nf-core/proteinfold/nextflow.config
Aug-31 10:34:13.550 [main] DEBUG nextflow.config.ConfigParserFactory - Using config parser v2
Aug-31 10:34:13.561 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Aug-31 10:34:14.486 [main] ERROR nextflow.cli.Launcher - Config parsing failed
nextflow.exception.ConfigParseException: Config parsing failed
at nextflow.config.parser.v2.ConfigParserV2.parse(ConfigParserV2.groovy:162)
at nextflow.config.parser.v2.ConfigDsl.includeConfig(ConfigDsl.groovy:262)
at nextflow.config.parser.v2.ConfigDsl.includeConfig(ConfigDsl.groovy:237)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at _nf_config_40053600fc77074f.run(_nf_config_40053600fc77074f:627)
at nextflow.config.parser.v2.ConfigParserV2.parse(ConfigParserV2.groovy:152)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.parser.v2.ConfigParserV2.parse(ConfigParserV2.groovy:192)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.parse0(ConfigBuilder.groovy:456)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:441)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:397)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:336)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:808)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:821)
at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
at nextflow.cli.Launcher.run(Launcher.groovy:526)
at nextflow.cli.Launcher.main(Launcher.groovy:686)
Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
_nf_config_d751873abab2694d: 40: If statements cannot be mixed with config statements @ line 40, column 9.
if (params.use_gpu) {
^
1 error
at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:292)
at org.codehaus.groovy.control.ErrorCollector.addFatalError(ErrorCollector.java:148)
at nextflow.config.parser.ConfigAstBuilder.collectSyntaxError(ConfigAstBuilder.java:1407)
at nextflow.config.parser.ConfigAstBuilder.invalidStatement(ConfigAstBuilder.java:340)
at nextflow.config.parser.ConfigAstBuilder.configBlockStatement(ConfigAstBuilder.java:303)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:214)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1716)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:570)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:560)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:635)
at java.base/java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:291)
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:652)
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:658)
at java.base/java.util.stream.ReferencePipeline.toList(ReferencePipeline.java:663)
at nextflow.config.parser.ConfigAstBuilder.configSelector(ConfigAstBuilder.java:320)
at nextflow.config.parser.ConfigAstBuilder.configBlockStatement(ConfigAstBuilder.java:297)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:214)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1716)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:570)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:560)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:635)
at java.base/java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:291)
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:652)
at java.base/java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:658)
at java.base/java.util.stream.ReferencePipeline.toList(ReferencePipeline.java:663)
at nextflow.config.parser.ConfigAstBuilder.configBlock(ConfigAstBuilder.java:277)
at nextflow.config.parser.ConfigAstBuilder.configStatement(ConfigAstBuilder.java:212)
at nextflow.config.parser.ConfigAstBuilder.compilationUnit(ConfigAstBuilder.java:188)
at nextflow.config.parser.ConfigAstBuilder.buildAST(ConfigAstBuilder.java:177)
at nextflow.config.parser.ConfigParserPlugin.buildAST(ConfigParserPlugin.java:51)
at org.codehaus.groovy.control.SourceUnit.buildAST(SourceUnit.java:256)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1939)
at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:803)
at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:631)
at nextflow.config.parser.v2.ConfigCompiler.compile0(ConfigCompiler.java:112)
at nextflow.config.parser.v2.ConfigCompiler.compile(ConfigCompiler.java:97)
at nextflow.config.parser.v2.ConfigParserV2.parse(ConfigParserV2.groovy:141)
... 22 common frames omitted
I'm not sure if the error occurs because I'm not configuring properly, or a problem with the pipeline.
If there is any more information I can provide, please let me know. Thank you in advance for your reply
Kind regards
Dear
When trying to run the nf-core proteinfold pipeline, I quickly run into the following error before the pipeline starts:
The full log looks as follows:
I'm not sure if the error occurs because I'm not configuring properly, or a problem with the pipeline.
If there is any more information I can provide, please let me know. Thank you in advance for your reply
Kind regards