nf-core download: customise config to include path to singularity image

[ewels]

We can run nf-core download <pipeline> --singularity to fetch the pipeline files and singularity image.

The code nicely edits the pipeline nextflow.config file so that the custom configs path is relative to the pipeline code for the institutional configs. However, this is not done for the singularity path, so the user still has to use -with-singularity to specify the location for these images.
It would be nice if the tool could edit the configs somehow so that the singularity image is automatically found with just -profile singularity.

Could potentially do this with process.container, or maybe be more clever & generic by setting the singularity cache directory path or something?

[maxulysse]

We could maybe play with singularity.cacheDir.
By default they are in work/singularity
We can change that, or download the singularity images there.

Who is using nf-core download to get singularity images?

[ewels]

We will hopefully use it for irma soon :)

[maxulysse]

Yes, but then we don't really need to download the singularity images with nf-core download, but we still would want to set up the path.

EDIT: nevermind, it should be in the confis

[ewels]

Just need to update this function to also edit process.container I guess? Or something similar..

tools/nf_core/download.py

Lines 226 to 243 in ebf6309

	def wf_use_local_configs(self):
	"""Edit the downloaded nextflow.config file to use the local config files
	"""
	nfconfig_fn = os.path.join(self.outdir, 'workflow', 'nextflow.config')
	find_str = 'https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}'
	repl_str = '../configs/'
	logging.debug("Editing params.custom_config_base in {}".format(nfconfig_fn))
	# Load the nextflow.config file into memory
	with open(nfconfig_fn, 'r') as nfconfig_fh:
	nfconfig = nfconfig_fh.read()
	# Replace the target string
	nfconfig = nfconfig.replace(find_str, repl_str)
	# Write the file out again
	with open(nfconfig_fn, 'w') as nfconfig_fh:
	nfconfig_fh.write(nfconfig)

[ewels]

Ok, after a bit of testing trial and error, this little gem seems to do the job:

singularity.cacheDir = "${projectDir}/../singularity-images/"

I think we're on to a winner 🎉

[ewels]

Implemented in the upcoming v1.13 release of tools. See #832.