Issue

After Nextflow 25.04 was released, many users reported getting .command.run: Permission denied errors immediately after launching recent pipeline versions of nf-core pipelines. This is an obscure error that emerged due to an unfortunately invalid configuration syntax in the nf-core pipeline template, that no longer works due to a stricter configuration parsing in the most recent Nextflow versions.

Resolution

If you’re seeing this above error you have a few options. In order of difficulty:

• Use an older version of Nextflow (24.10.6 or earlier)

• Use a Nextflow config file that overwrites the invalid config syntax locally. Save this in a config file

    // Set bash options
  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
  ]

  and use with -c, eg. nextflow run nf-core/rnaseq -c nf_config_fix.config.

• Use an older version of the pipeline that has nf-core/tools template < 3.0.0, thus was published before 2024-10-08. The issue was fixed and published in the template 3.1.2 on 2025-01-27, so pipeline versions released after that day are mostly not affected either, unless they were published with an older template. You can fine the template version that a pipeline uses in a hidden file called .nf-core.yml in the pipeline repository. Additionally, some pipelines already incorporate a manual fix, so even though released during that period, pixelator v1.4.0 and references 0.1 already incorporate the required change.