Fix some merge bugs

[allyhawkins]

In merging the processed data for a project for the Portal, I came across a small error in the merge_sces.R script. R was complaining about calculating the sum() of a list so I just added an unlist() and that fixed that problem.

The other precautionary measure I took here is to ensure that if a processed file exists but its size is 0, it's not actually included in the merging process. I can imagine that causing problems down the line if we try to read in an empty file. I also added a warning message that should print out any libraries that are not going to be included in the object.

[jashapiro]

These seem like good things to catch! I had a different option for the first, up to you. But the second I think we want something a bit different?

[jashapiro]

This is a bit more descriptive, I think?

Suggested change

	purrr::map(\(sce) "adt" %in% altExpNames(sce)) |>
	unlist()
	purrr::map_lgl(\(sce) "adt" %in% altExpNames(sce))

[jashapiro]

Fixing the indentation, but I think the message here is a bit confusing, as there are processed files for multiplexed data, which will be listed again here, along with all of the spatial an bulk libraries.

Suggested change

	libraries_ch
	.filter{!(it.library_id in merge_libaries.getVal())}
	.subscribe{
	log.warn("Processed files do not exist for ${it.library_id}. This library will not be included in the merged object.")
	}
	libraries_ch
	.filter{!(it.library_id in merge_libaries.getVal())}
	.subscribe{
	log.warn("Processed files do not exist for ${it.library_id}. This library will not be included in the merged object.")
	}

If you want to look for files without processed samples, I think you would have to do that more directly, maybe with a duplicate filter to the one below looking at the files themselves? Something like:

filtered_libraries_ch.single_sample
  .map{
        it.library_id,
        file("${params.results_dir}/${it.project_id}/${it.sample_id}/${it.library_id}_processed.rds")
      ]}
  .filter{!(it[1].exists() && it[1].size() > 0)}
  .subscribe{
      log.warn("Processed files do not exist for ${it[0]}. This library will not be included in the merged object.")
    }

[allyhawkins]

Thanks for the suggestions @jashapiro. I went ahead and incorporated both of them, I think we do want to avoid printing out multiplexed samples in the error message.

[jashapiro]

LGTM