Hi folks If you have recently updated Nextflow to the `25 04 nf-core #announcements

Hi folks! If you have recently updated Nextflow to...

Phil Ewels

05/15/2025, 9:47 AM

Hi folks! If you have recently updated Nextflow to the

25.04

release and started getting

.command.run: Permission denied

errors, please read! This is an obscure error that has already been fixed, but lingers in a few pipelines. If you're this above error you have a few options. In order of difficulty: • Use an older version of Nextflow • Use a Nextflow config file that overwrites the invalid config syntax locally (see thread for details 🧵) • Use an older version of the pipeline that has nf-core/tools template < 3.0.0 Of course, the faster that pipeline maintainers can release new versions of their pipeline with the included fix from #CE5LG7WMB template 3.2.0, the better! See the thread for some more detail 🧵

thankyou 2

👍 2

nf core pet 3

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Phil Ewels

05/15/2025, 9:47 AM

If you want to use a local config file to fix, it should be:

Copy code

// 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 
 ]

Save this in a config file and use with

-c

, eg.

nextflow run nf-core/rnaseq -c nf_config_fix.config ...

❤️ 1

catjam 2

Phil Ewels

05/15/2025, 9:47 AM

The history of how this came about is: • We tweaked the

process.shell

config option in the nf-core template, back in v3.0.0 • Turns out that the syntax we used (a multi-line string) wasn't supported and shouldn't really have worked, but by chance it did so everyone was happy • Nextflow

24.12.0-edge

and later made a small change to how the

.command.run

files are generated, resulting in the above error with our config syntax • We figured it out and fixed it in January, and updated the template in tools v3.2.0

Phil Ewels

05/15/2025, 9:48 AM

See https://github.com/nf-core/tools/pull/3416 for discussion and the fix that went into the nf-core template

Phil Ewels

05/15/2025, 9:53 AM

This is the same thing that was discussed in January due to breaking CI tests for pipelines, see thread in #C04QR0T3G3H here.

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