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Digital Trials pipeline configured for WES

Browse Source 
Source-only snapshot of the cluster branch for WES execution. Large
reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are
omitted: they are baked into the container images at build time and
mounted from the dreamdock-data PVC at runtime, and exceed the Gitea
request size limit.

Pipeline entry point is main.nf, which orchestrates the biotransformer,
conplex and tissue modules as a single workflow. Ligand inputs are read
from the eureka workspace; protein_zarr and chembl_db come from the
dreamdock-data PVC.
This commit is contained in:
Olamide Isreal
2026-07-27 21:59:52 +01:00
commit 9e75f44f1a
86 changed files with 10142 additions and 0 deletions
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78
nf_metabol_screen_adaptive/.nextflow.log.6 Normal file
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Jul-03 12:08:15.992 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-03 12:08:16.116 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Jul-03 12:08:16.165 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/omic/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1
Jul-03 12:08:16.218 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-03 12:08:16.219 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-03 12:08:16.223 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-03 12:08:16.239 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-03 12:08:16.269 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:16.274 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:16.319 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Jul-03 12:08:16.323 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1ddd3478] - activable => nextflow.secret.LocalSecretsProvider@1ddd3478
Jul-03 12:08:16.339 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-03 12:08:17.003 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-03 12:08:17.044 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-03 12:08:17.064 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [insane_snyder] DSL2 - revision: 49b8a74e0c
Jul-03 12:08:17.066 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-03 12:08:17.066 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-03 12:08:17.150 [main] DEBUG nextflow.Session - Session UUID: 8cc53326-d69c-4269-9519-4eb256ccbbd2
Jul-03 12:08:17.151 [main] DEBUG nextflow.Session - Run name: insane_snyder
Jul-03 12:08:17.152 [main] DEBUG nextflow.Session - Executor pool size: 80
Jul-03 12:08:17.163 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-03 12:08:17.180 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:17.322 [main] DEBUG nextflow.cli.CmdRun -
Version: 25.04.3 build 5949
Created: 02-06-2025 20:56 UTC
System: Linux 6.11.0-26-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-Ubuntu-0ubuntu124.04
Encoding: UTF-8 (UTF-8)
Process: 3786432@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (220.7 GB) - Swap: 0 (0)
Jul-03 12:08:17.386 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/metabolite-screen/nf_metabol_screen/work [btrfs]
Jul-03 12:08:17.386 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /data/bugra/metabolite-screen/nf_metabol_screen/bin
Jul-03 12:08:17.401 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-03 12:08:17.413 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-03 12:08:17.440 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-03 12:08:17.469 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-03 12:08:17.483 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Jul-03 12:08:17.707 [main] DEBUG nextflow.Session - Session start
Jul-03 12:08:17.717 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugra/metabolite-screen/nf_metabol_screen/execution_trace.txt
Jul-03 12:08:17.950 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-03 12:08:18.079 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e80a6c5924994093: /data/bugra/metabolite-screen/nf_metabol_screen/test.nf
Script_181c5ac3efe09ab5: /data/bugra/metabolite-screen/nf_metabol_screen/main.nf
Jul-03 12:08:18.081 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: chunks for class: nextflow.script.WorkflowBinding
Jul-03 12:08:18.096 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: chunks for class: nextflow.script.WorkflowBinding
at groovy.lang.Binding.getVariable(Binding.java:61)
at nextflow.script.WorkflowBinding.getVariable(WorkflowBinding.groovy:143)
at groovy.lang.Binding.getProperty(Binding.java:117)
at nextflow.script.WorkflowBinding.getProperty(WorkflowBinding.groovy:132)
at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:167)
at groovy.lang.Closure.getPropertyTryThese(Closure.java:325)
at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:315)
at groovy.lang.Closure.getProperty(Closure.java:301)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at Script_e80a6c5924994093$_runScript_closure1$_closure2.doCall(Script_e80a6c5924994093:13)
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:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at groovy.lang.Closure.call(Closure.java:433)
at groovy.lang.Closure.call(Closure.java:412)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.script.BaseScript.run0(BaseScript.groovy:182)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.script.BaseScript.run(BaseScript.groovy:193)
at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246)
at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:246)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
at nextflow.cli.CmdRun.run(CmdRun.groovy:379)
at nextflow.cli.Launcher.run(Launcher.groovy:513)
at nextflow.cli.Launcher.main(Launcher.groovy:673)