Survey Transcritome Indices for new airway pathogens

[davidsmejia]

Context

https://github.com/AlexsLemonade/refinebio/pull/3366

This issue is to track the creation of survey jobs for transcriptome indices required to process samples of requested airway pathogens.

The new pathogens:

• Staphylococcus aureus
• Streptococcus pneumoniae
• Stenotrophomonas maltophilia
• Aspergillus fumigatus
• Klebsiella pneumoniae

Problem or idea

After merging the referenced PR into dev, we should test that we can generate these transcriptome indices and then process a sample using them on staging.

Example command to run on foreman instance.

./foreman/run_management_command.sh survey_all --accession "Staphylococcus aureus, EnsemblBacteria"

Note: Aspergillus fumigatus is part of the EnsemblFungi division.

Solution or next step

• [ ] Create transcriptome indices on staging
• [x] Create transcriptome indices on prod

[davidsmejia]

I created these on production, after considering it for a bit I realized that it will be fine to run these on prod and if not successful we can iterate fixes on staging. However these were queued just fine.