Description of the bug
Encountering a MissingMethodException when executing the nf-core/mag pipeline, specifically related to the java.util.LinkedList.getFileSystem().
Steps to Reproduce
- Command used to run the pipeline:
nextflow run nf-core/mag -profile docker --input 'fastq_files/*.fastq.gz' --outdir mag-results
Program output
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/nf-core/mag` [mighty_carlsson] DSL2 - revision: ba72349594 [master]
ERROR ~ Unknown method invocation `getFileSystem` on LinkedList type
-- Check '.nextflow/assets/nf-core/mag/main.nf' at line: 44 or '.nextflow.log' for more details
Extract from .nextflow.log:
Nov-07 03:45:27.972 [main] DEBUG nextflow.Session - Session aborted -- Cause: No signature of method: java.util.LinkedList.getFileSystem() is applicable for argument types: () values: []
Nov-07 03:45:27.986 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingMethodException: No signature of method: java.util.LinkedList.getFileSystem() is applicable for argument types: () values: []
Running with docker/test profiles worked:
nextflow run nf-core/mag -profile docker,test --outdir mag-test
Environment
Java Version
openjdk version "11.0.20" 2023-07-18 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.20.0.8-1.amzn2.0.1) (build 11.0.20+8-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.20.0.8-1.amzn2.0.1) (build 11.0.20+8-LTS, mixed mode, sharing)
Nextflow version
version 23.10.0 build 5889
created 15-10-2023 15:07 UTC
System information
Linux ip-172-31-37-92.ec2.internal 5.10.198-187.748.amzn2.x86_64 #1 SMP Tue Oct 24 19:49:54 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Description of the bug
Encountering a
MissingMethodExceptionwhen executing the nf-core/mag pipeline, specifically related to thejava.util.LinkedList.getFileSystem().Steps to Reproduce
nextflow run nf-core/mag -profile docker --input 'fastq_files/*.fastq.gz' --outdir mag-resultsProgram output
Extract from .nextflow.log:
Running with docker/test profiles worked:
Environment
Java Version
Nextflow version
System information