wildcard expansion triggering "argument too long" error

[tom-brekke]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

The wildcard-expansion in the gzip call here:

modules/modules/nf-core/vsearch/cluster/main.nf

Line 63 in 805dff3

gzip -n ${prefix}.${out_ext}*

is running up against the limit on the maximum number of arguments in my OS.

I would like to replace it with something like this instead:

find . -name \"${prefix}.${out_ext}*[0-9]\" | xargs gzip -n

I've implemented this locally and it seems to work.
I'm beginning a PR that I'll link to presently.

Command used and terminal output

Relevant files

No response

System information

Nextflow version 24.10.5
HPC
slurm
Apptainer
Debian GNU/Linux
ampliseq version 2.13.0

[tom-brekke]

Here's the PR: #8307