Hi! Is there a way to avoid the

test_stub_gzip_syntax

test in

nf-core modules lint

for a specific module? I'm modifying a module to use pigz as a replacement for gzip. The thing is I'm using wave containers, which apparently do not ship

gzip

. So I would like my stub command to be:

stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    echo "" | pigz > ${prefix}.fastq.gz
    """

but when linting I get the error:

test_stub_gzip_syntax: Stub gzip files must use 'echo "" | gzip >' syntax. Invalid patterns found: echo "" | pigz > ${prefix}.fastq.gz

I'd like to avoid installing

gzip

in the module just because of that... Thanks a lot!

the latest dev version of tools (

pip install --upgrade --force-reinstall git+<https://github.com/nf-core/tools.git@dev>

) extends the baseimage with gzip

I installed this version, but I still get

.command.sh: line 2: gzip: command not found

with:

nf-core modules test <tool>

did you run

nf-core modules container create

to regenerate the containers with the new baseimage?

hum no... I thought you were talking about on the fly extension of the base image. I did not think you were referring to building a new image 🤔 It works like a charm now, thanks!