***UNCHECKED*** Nextflow within galaxy

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***UNCHECKED*** Nextflow within galaxy

Luc Cornet
Hi everyone,

I would like to run a Netxflow script in galaxy (yes I know it’s strange).
So I made a test but I have a problem that I don’t undertstand, I am able to launch my Nextflow tool in galaxy but not to complete the analysis.

The log out of galaxy :

  >  juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work [Mac OS X]
    juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
    juil.-07 19:28:53.988 [main] DEBUG nextflow.Session - Session start invoked
    juil.-07 19:28:54.296 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
    juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    juil.-07 19:28:54.372 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
    juil.-07 19:28:54.375 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
    juil.-07 19:28:54.446 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4
    juil.-07 19:28:54.477 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
    juil.-07 19:28:54.477 [main] DEBUG nextflow.Session - Session await
    juil.-07 19:28:54.579 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    juil.-07 19:28:54.584 [Task submitter] INFO  nextflow.Session - [37/23b693] Submitted process > Testo
    juil.-07 19:28:54.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: Testo; status: COMPLETED; exit: 0; error: -; workDir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work/37/23b693d7b8dbbf227f19b3dd9780a7]
    juil.-07 19:28:54.674 [main] DEBUG nextflow.Session - Session await > all process finished
    juil.-07 19:28:54.675 [main] DEBUG nextflow.Session - Session await > all barriers passed
    juil.-07 19:28:54.682 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms]
    juil.-07 19:28:54.855 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
    juil.-07 19:28:54.869 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye


And the log in galaxy:

    > juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/27/working/work [Mac OS X]
    juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
    juil.-08 11:38:10.001 [main] DEBUG nextflow.Session - Session start invoked
    juil.-08 11:38:10.373 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
    juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    juil.-08 11:38:10.455 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
    juil.-08 11:38:10.458 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
    juil.-08 11:38:10.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4
    juil.-08 11:38:10.591 [main] DEBUG nextflow.script.ScriptRunner - > Await termination


Can someone help me with this ?

Best,
Luc

------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
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