Hi all, I'm seeing a process.shell error on version 4.2.0. I'm getting this error with my data as well as the test data. Executed like this

nextflow run nf-core/airrflow -r 4.2.0 -profile test,singularity -c belfer.config --outdir results_test

The error message is like this:

ERROR ~ Error executing process > 'NFCORE_AIRRFLOW:AIRRFLOW:DATABASES:UNZIP_REFERENCE_FASTA (unzip_db)'

Caused by:
  Directive `process.shell` cannot contain new-line characters - offending value: [bash

  set -e # Exit if a tool returns a non-zero status/exit code
  set -u # Treat unset variables and parameters as an error
  set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
  set -C # No clobber - prevent output redirection from overwriting files.
  ]



 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
-[nf-core/airrflow] Pipeline completed with errors-

Reverting to version 4.1.0 resolved the error. I suspect a typo somewhere, e.g. the settings for process.shell?

Hi Ashley, I just tried it and it worked fine for me. Are you on the latest Nextflow version?

Hey, I encountered the same problem and solved it by changing the process.shell directive to the new way:

process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

I think this will be changed with the template update to 3.2.0 anyways.

Thanks @Famke Bäuerle, just to confirm this will be fixed in the upcoming 4.3.0 release with the template update!