CI
b533a32bc8
Build pipeline: vsh-ci-template-7m7cc
Source commit: 73b07a96e0
Source message: Fix quotes in test (#4)
* Fix quotes in test
* query the first output file to pick up the 'name' value again and output it
grep with start and end position constaints
51 lines
5.4 KiB
Plaintext
51 lines
5.4 KiB
Plaintext
Jun-25 12:24:34.214 [main] DEBUG nextflow.cli.Launcher - $> nextflow -q run /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf --resourcesDir /opt/viash_tools/target/native/nextflow/generate_schema_v9 --input /workdir/root/repo/src/yq/config.vsh.yaml --output target/nextflow/yq/nextflow_schema.json --add_global_params true --enable_dataset_input false
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Jun-25 12:24:34.429 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
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Jun-25 12:24:34.493 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
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Jun-25 12:24:34.534 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
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Jun-25 12:24:34.535 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
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Jun-25 12:24:34.542 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
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Jun-25 12:24:34.596 [main] INFO org.pf4j.AbstractPluginManager - No plugins
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Jun-25 12:24:34.693 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /workdir/root/repo/nextflow.config
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Jun-25 12:24:34.704 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workdir/root/repo/nextflow.config
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Jun-25 12:24:34.760 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json
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Jun-25 12:24:34.767 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2e647e59] - activable => nextflow.secret.LocalSecretsProvider@2e647e59
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Jun-25 12:24:34.800 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
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Jun-25 12:24:36.250 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
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Jun-25 12:24:36.293 [main] INFO nextflow.cli.CmdRun - Launching `/opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf` [cheeky_lavoisier] DSL2 - revision: 513aeab0c0
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Jun-25 12:24:36.308 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
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Jun-25 12:24:36.309 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
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Jun-25 12:24:36.533 [main] DEBUG nextflow.Session - Session UUID: 8c0657a5-f61b-4b51-b7dc-a023ac27ee7c
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Jun-25 12:24:36.534 [main] DEBUG nextflow.Session - Run name: cheeky_lavoisier
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Jun-25 12:24:36.535 [main] DEBUG nextflow.Session - Executor pool size: 4
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Jun-25 12:24:36.561 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
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Jun-25 12:24:36.592 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
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Jun-25 12:24:36.654 [main] DEBUG nextflow.cli.CmdRun -
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Version: 24.04.2 build 5914
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Created: 29-05-2024 06:19 UTC
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System: Linux 6.1.85+
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Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.10+7-LTS
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Encoding: UTF-8 (UTF-8)
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Process: 239@vsh-ci-template-7m7cc-nxf-generate-schemas-382080591 [10.48.2.43]
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CPUs: 4 - Mem: 15.6 GB (838.7 MB) - Swap: 0 (0)
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Jun-25 12:24:36.744 [main] DEBUG nextflow.Session - Work-dir: /workdir/root/repo/work [ext2/ext3]
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Jun-25 12:24:36.745 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /opt/viash_tools/target/native/nextflow/generate_schema_v9/bin
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Jun-25 12:24:36.769 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
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Jun-25 12:24:36.807 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
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Jun-25 12:24:36.905 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
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Jun-25 12:24:36.947 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000
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Jun-25 12:24:37.183 [main] DEBUG nextflow.Session - Session start
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Jun-25 12:24:38.920 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
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Jun-25 12:24:41.528 [main] DEBUG nextflow.Session - Workflow process names [dsl2]:
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Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Igniting dataflow network (0)
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Jun-25 12:24:41.529 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
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Script_85cbbb9c9058ccbe: /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf
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Script_a1b09e222ee37273: /opt/viash_tools/target/native/nextflow/generate_schema_v9/WorkflowHelper_v9.nf
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Jun-25 12:24:41.529 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
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Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await
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Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await > all processes finished
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Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await > all barriers passed
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Jun-25 12:24:41.543 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
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Jun-25 12:24:41.569 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
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Jun-25 12:24:41.601 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
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Jun-25 12:24:41.601 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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