Add functionality for --unknown-slide in spaceranger/count
#7233
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Add functionality to be able to use the `--unknown-slide` option of Space Ranger Count, specified using the `slide` column in the input samplesheet.
fasterius
changed the title
--unknown-slide option--unknown-slide in spaceranger/count
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While the Conda tests are expected to fail (is there a way to disable Conda for some modules?), I'm not sure why some of the other tests are failing. Some seem to have run out of memory, while others reach an unexpected EOF when pulling the Docker image. The linting is also failing in a weird manner, saying it can't connect to the Docker image URL, while it clearly works fine for some most tests. Any ideas? |
| def slide = meta.slide ? meta.slide : "" | ||
| def area = meta.area ? meta.area : "" | ||
| if (slide.matches("visium-(.*)") && area == "" && slidefile == "") { | ||
| slide_and_area = "--unknown-slide=\"${slide}\"" |
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Would --unknown-slide take any arguments? I thought it's a boolean flag.
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It's not a boolean, it takes visium-[1,2,2-large,hd] as argument.
| def slide = meta.slide ? meta.slide : "" | ||
| def area = meta.area ? meta.area : "" | ||
| if (slide.matches("visium-(.*)") && area == "" && slidefile == "") { | ||
| slide_and_area = "--unknown-slide=\"${slide}\"" | ||
| } else { | ||
| slide_and_area = "--slide=\"${slide}\" --area=\"${area}\"" | ||
| } |
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Do we need this at all? We could also rely on the pipeline developers to specify --area etc. via task.ext.args, e.g.
process {
withName: SPACERANGER_COUNT {
task.ext.args = { (meta.slide & meta.area) ? "--area=\"${meta.area}\" --slide=\"${meta.slide}\"" : "--unknown-slide" }
}}
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Yes, I did think about this, but since this is specifically part of the Space Ranger Count software as an explicit option, I thought it made more sense to have it in the module itself. It's also required to actually specify the version of Visium being run (e.g. --unknown-slide visium-1), which is also a demand of the software itself. It felt odd to me to write something so software-specific outside of the software module.
just restarted the checks, let's see |
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Great! Any ideas regarding the failing tests/linting? I'm still seeing the same errors. |
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unfortunately not... best to ask around on slack I guess. |
There is an option to for Space Ranger Count to run without knowing the exact slide,
--unknown-slide, that has been requested by users (see nf-core/spatialvi#99 (comment)). This PR adds this to thespaceranger/countmodule, which uses the already existingmeta.slidevalue as input.This would work well for the
nf-core/spatialvipipeline, since no other changes would need to be done; rather than specifying a slide (e.g.H1-VJQNJXM) in theslidesamplesheet column the user would specifyvisium-[1,2,2-large,hd]and leave theareacolumn empty. I'm sure there are other ways of doing it, though, and would be happy to change it if somebody thinks another solution would be better.PR checklist