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Tweak to celltype annotation #21

Merged
merged 4 commits into from
Jun 12, 2024
Merged

Tweak to celltype annotation #21

merged 4 commits into from
Jun 12, 2024

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Tobi1kenobi
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Modifications:

  • Added parameter to enable or disable printing of celltypist probabilities per sample and annotation. This cuts down on file usage in yascp runs with hundreds of samples and many models
  • Modified celltype merge input to take a TSV with filenames rather than print filenames to a terminal command which broke with many models and samples
  • Fixed merging of celltype models when using yascp fetch full_name_inputs.tsv file by making the string splitting more flexible.

Notes:

  • Celltype merge TSVs save as a result rather than in the hashed work directory because of issues printing to a file that was in the current work dir. Files could be deleted within the nextflow process but as it stands, are not.
  • Merging of celltype models should work with full_names_inputs.tsv and original sample_ids but the latter is untested. Also untested is on multiplexed samples.
  • I believe a bug still exists when submitting multiple samples with the same sanger_sample_id e.g. resequenced samples. For celltype annotation I think Azimuth is broken for these samples whilst celltypist and keras work the normalisation may be done within sanger_sample_id rather than within each sequenced sample. tl;dr sample duplicates not handled well

@maxozo maxozo merged commit 9997239 into wtsi-hgi:v1.6 Jun 12, 2024
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