[BUG] Cannot invoke method containsKey() on null object

[AlinaKurjan]

Describe the bug Cannot run VSN-pipelines with any files due to the same error occurring regardless of the pipeline being run OR the file input format.

To Reproduce Steps to reproduce the behavior:

1. Configure with these options:

   nextflow config vib-singlecell-nf/vsn-pipelines \ -profile tenx,singularity,hg38,single_sample > single_sample.config

   automatically generated config file always has a Warning message at the end saying the following: "WARN: Unknown config attribute params.global.outdir -- check config file: /home/a/akurjan/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/nextflow.config"

2. Run using this entry point:

   NXF_VER=21.04.3 nextflow -C single_sample.config run vib-singlecell-nf/vsn-pipelines -entry single_sample

3. See error:

   N E X T F L O W  ~  version 21.04.3
   Launching `vib-singlecell-nf/vsn-pipelines` [boring_bardeen] - revision: 6a9c70769b [master]
   Cannot invoke method containsKey() on null object
   
   -- Check script '/home/a/akurjan/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/./src/channels/channels.nf' at line: 39 or see '.nextflow.log' file for more details

Screenshots If applicable, add screenshots to help explain your problem.

Please complete the following information:

• System: Linux 3.10.0-1160.59.1.el7.x86_64
• Nextflow Version: 22.04.0 (but running specifically the 21.04.3 version required by the config file)
• vsn-pipelines Version: latest available

Additional context .nextflow.log:

Version: 21.04.3 build 5560
  Created: 21-07-2021 15:09 UTC (16:09 BST)
  System: Linux 3.10.0-1160.59.1.el7.x86_64
  Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21
  Encoding: UTF-8 (UTF-8)
  Process: 36005@cbrglogin3 [10.10.1.198]
  CPUs: 40 - Mem: 1007.6 GB (227.3 GB) - Swap: 1024 GB (751.4 GB)
Jun-10 13:00:10.172 [main] DEBUG nextflow.Session - Work-dir: /t1-data/project/tendonhca/shared/chromium/analysis/alina/wo$
Jun-10 13:00:10.173 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/a/akurjan$
Jun-10 13:00:10.188 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-10 13:00:10.203 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-10 13:00:10.541 [main] DEBUG nextflow.Session - Session start invoked
Jun-10 13:00:10.548 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /t1-data/project/tendonhc$
Jun-10 13:00:12.165 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-10 13:00:16.234 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: COMPRESS_HDF5, SC__FILE_CONVERTER_FROM_$
Jun-10 13:00:36.925 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method containsKey() on null o$
Jun-10 13:00:36.953 [main] DEBUG nextflow.Session - The following nodes are still active:
  [operator] view

Jun-10 13:00:36.968 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot invoke method containsKey() on null object
        at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)

etc.

[gomeznick86]

@AlinaKurjan were you able to solve this? I'm having the same issue.

[AlinaKurjan]

@AlinaKurjan were you able to solve this? I'm having the same issue.

Unfortunately not, had to do steps manually in the end.