Simplify inputs and outputs for singler #478
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Also add in example of how to join in outputs at the end (enabling separation for cellassign)
sjspielman
approved these changes
Oct 2, 2023
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| meta.celltype_publish_dir = "${params.checkpoints_dir}/celltype/${meta.library_id}"; | ||
| meta.singler_dir = "${meta.celltype_publish_dir}/${meta.library_id}_singler"; | ||
| meta.cellassign_dir = "${meta.celltype_publish_dir}/${meta.library_id}_cellassign"; | ||
| meta.singler_model_file = singler_model_file; | ||
| meta.cellassign_reference_file = cellassign_reference_file; | ||
| meta.cellassign_reference_name = cellassign_reference_name; | ||
| // return simplified input: | ||
| [meta, processed_sce] |
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so this syntax is augmenting meta as an "intermediate" step before returning [meta, processed_sce]
| singler_input_ch = celltype_input_ch | ||
| // add in singler model or empty file | ||
| .map{it.toList() + [file(it[0].singler_model_file ?: empty_file)]} |
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Ah I see, so we have the nulls back above, and this file-ifies.
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Yes, and the reason for this is that we don't want to store file objects in the metadata: just strings.
| tuple val(meta), path(processed_rds), | ||
| path(cellassign_reference_file), val(cellassign_reference_name), | ||
| path(singler_dir) | ||
| tuple val(meta.library_id), path(singler_dir) |
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So here is an option to make the inputs to the singler step a bit simpler.
I also simplified the outputs to just the library id and the output directory, because I realized if we do them right the join at the end for the final annotation step could be pretty easy, and I included an example of how that would look.
If we follow that patter, we could actually make the cellassign step fully separate, rather than passing in the outputs from singleR. I don't think it matters much: but it might be a bit simpler and a tiny bit more efficient.
I also commented out the final output chunk because I was getting some odd and intermittent errors there that I couldn't figure out... something about concurrent modifications, but the fact that it was intermittent (though never in CI) was making me crazy.