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Digital Trials pipeline configured for WES

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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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69
nf_metabol_screen_adaptive/.nextflow.log.5 Normal file
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Jul-03 12:08:35.777 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile docker test.nf
Jul-03 12:08:35.914 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3
Jul-03 12:08:35.944 [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 12:08:35.978 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-03 12:08:35.979 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-03 12:08:35.983 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-03 12:08:35.996 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-03 12:08:36.024 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:36.028 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /data/bugra/metabolite-screen/nf_metabol_screen/nextflow.config
Jul-03 12:08:36.073 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/omic/.nextflow/secrets/store.json
Jul-03 12:08:36.078 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@29314cc9] - activable => nextflow.secret.LocalSecretsProvider@29314cc9
Jul-03 12:08:36.086 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jul-03 12:08:36.792 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [k8s, docker]
Jul-03 12:08:36.833 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Jul-03 12:08:36.850 [main] DEBUG nextflow.cli.CmdRun - Launching `test.nf` [insane_woese] DSL2 - revision: 063b5cd9a9
Jul-03 12:08:36.852 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-03 12:08:36.852 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-03 12:08:36.922 [main] DEBUG nextflow.Session - Session UUID: a62b6efd-60bb-4b97-a6e1-a68592f7d53f
Jul-03 12:08:36.923 [main] DEBUG nextflow.Session - Run name: insane_woese
Jul-03 12:08:36.923 [main] DEBUG nextflow.Session - Executor pool size: 80
Jul-03 12:08:36.935 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-03 12:08:36.943 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:36.975 [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: 3786813@k8s-node23 [127.0.1.1]
CPUs: 80 - Mem: 251.6 GB (220.6 GB) - Swap: 0 (0)
Jul-03 12:08:37.006 [main] DEBUG nextflow.Session - Work-dir: /data/bugra/metabolite-screen/nf_metabol_screen/work [btrfs]
Jul-03 12:08:37.007 [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 12:08:37.022 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-03 12:08:37.034 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-03 12:08:37.060 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Jul-03 12:08:37.087 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-03 12:08:37.098 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 81; maxThreads: 1000
Jul-03 12:08:37.228 [main] DEBUG nextflow.Session - Session start
Jul-03 12:08:37.233 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/bugra/metabolite-screen/nf_metabol_screen/execution_trace.txt
Jul-03 12:08:37.394 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-03 12:08:37.590 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-03 12:08:37.591 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-03 12:08:37.598 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-03 12:08:37.609 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=80; memory=251.6 GB; capacity=80; pollInterval=100ms; dumpInterval=5m
Jul-03 12:08:37.612 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jul-03 12:08:37.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'METABOLITE_SCREEN': maxForks=0; fair=false; array=0
Jul-03 12:08:37.724 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: METABOLITE_SCREEN
Jul-03 12:08:37.726 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-03 12:08:37.727 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > METABOLITE_SCREEN
Jul-03 12:08:37.728 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_181c5ac3efe09ab5: /data/bugra/metabolite-screen/nf_metabol_screen/main.nf
Script_3b80613f4955047b: /data/bugra/metabolite-screen/nf_metabol_screen/test.nf
Jul-03 12:08:37.728 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jul-03 12:08:37.728 [main] DEBUG nextflow.Session - Session await
Jul-03 12:08:38.010 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-03 12:08:38.016 [Task submitter] INFO nextflow.Session - [3d/10f68f] Submitted process > METABOLITE_SCREEN
Jul-03 12:08:44.784 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: METABOLITE_SCREEN; status: COMPLETED; exit: 0; error: -; workDir: /data/bugra/metabolite-screen/nf_metabol_screen/work/3d/10f68ffcfb09a7b35f3b90f43efbd9]
Jul-03 12:08:44.786 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-03 12:08:45.543 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-03 12:08:45.581 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-03 12:08:45.582 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-03 12:08:45.586 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Jul-03 12:08:45.596 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3.7s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=10 GB; ]
Jul-03 12:08:45.596 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-03 12:08:45.598 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-03 12:08:46.431 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-03 12:08:46.525 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-03 12:08:46.538 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-03 12:08:46.538 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye