collate_results fix

[mattssca]

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[rdmorin]

Please don't submit a PR until the problem is fully fixed. Use a draft PR instead if you want feedback on the partial fix. I also would like to see working examples that test both modes of from_cache in the PR.

[mattssca]

I have now marked this PR as a draft, I will update and provide the information you requested once it's ready for review. Thanks!

[mattssca]

This function has now been updated with appropriate file paths for reading and exporting cached results. The function has also been getting a facelift in terms of expanded in-line comments, parameter descriptions and extended examples.

When testing this function I was not allowed to write to file: Error: Cannot open file for writing

However, I tested this function with from_cached = FALSE and write_to_file = FALSE for both genome and capture with success. As such:

genome_collated = collate_results(seq_type_filter = "genome", from_cache = FALSE, write_to_file = FALSE)
capture_collated = collate_results(seq_type_filter = "capture", from_cache = FALSE, write_to_file = FALSE)

I also tested using these_samples_metadata and join_with_full_metadata:

fl_metadata = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL")
fl_collated = collate_results(seq_type_filter = "genome", join_with_full_metadata = TRUE, these_samples_metadata = fl_metadata, write_to_file = FALSE, from_cache = FALSE)

Lastly, I tested this function with using the sample_table parameter as well:

fl_samples = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") %>% dplyr::select(sample_id, patient_id, biopsy_id)
fl_collated = collate_results(sample_table = fl_samples, seq_type_filter = "genome", from_cache = FALSE, write_to_file = FALSE)