Non-CLI usage of nf-core download

[seedgeorge]

Description of feature

Hi there,

Currently the nf-core download command doesn't permit a parameter-based answer to to the Define $NXF_SINGULARITY_CACHEDIR f question that pops up on the command-line interface. For the purposes of putting this command in a script, it would be handy to not have to interact with a command line prompt at all.

Thanks for the useful tool!

[MatthiasZepper]

Sorry for the late reply.

Technically, this should already be the case. The code has a check that should prevent prompts from being shown in non-interactive sessions:

tools/nf_core/download.py

Lines 440 to 444 in 930ece5

	if (
	self.container_system == "singularity"
	and os.environ.get("NXF_SINGULARITY_CACHEDIR") is None
	and stderr.is_interactive # Use rich auto-detection of interactive shells
	):

Why this detection fails in your case, I can't tell. Have you tried to pipe the output to tee, cat or tail or something? At least the pipe should be detected, and any interactive prompts thus turned off.

[ewels]

Is there a reason that you can't provide it on the same line as the command? eg.

NXF_SINGULARITY_CACHEDIR="/path/to/cache" nf-core download

Then as @MatthiasZepper says, the interactive prompt shouldn't show. And it is not super different to using a flag with the path after the command.

[MatthiasZepper]

I presume, that the original poster does not want to define a cache directory?