Option to use the --unknown-slide parameter in spaceranger count

[pstorozenko]

Description of feature

Hi!
Thanks for the work on the pipeline!
I wonder if you ever considered adding the possibility to add the --unknown-slide parameter to the spaceranger count in the spatialvi pipeline?

Current design doesn't allow for it, and expects the slide and area parameters to be always present, not allowing to work with visium-1/2/2-large data.

spatialvi/modules/nf-core/spaceranger/count/main.nf

Lines 34 to 50 in f846f00

	"""
	spaceranger count \\
	--id="${prefix}" \\
	--sample="${meta.id}" \\
	--fastqs=. \\
	--slide="${meta.slide}" \\
	--area="${meta.area}" \\
	--transcriptome="${reference}" \\
	--localcores=${task.cpus} \\
	--localmem=${task.memory.toGiga()} \\
	$image $cytaimage $darkimage $colorizedimage \\
	$probeset \\
	$alignment \\
	$slidefile \\
	$args
	mv ${prefix}/outs outs

Best!

[fasterius]

Hi, @pstorozenko!

Sorry for the late reply, I've been on vacation. This is an issue with the spaceranger/count module itself, and not the spatialvi pipeline. I would recommend you to open an issue at the nf-core modules repository instead: https://github.com/nf-core/modules/issues. If the module is updated we can update the pipeline as well.