When TheiaCoV_ONT is run for flu (and maybe other organisms?), if the sample does not pass the read screening, the workflow fails and no information about reasons for failure is output to the Terra table.
:repeat: How to Reproduce
Terra on GCP
Presumably will only occur if there is little sequence data for a given sample, when running TheiaCoV_ONT for flu
Expect for the workflow to complete successfully, but for a read screening column to be created in the Terra data table that shows that read screening has failed. This should be for flu but also for other organisms
:floppy_disk: Version Information
TheiaCoV_ONT, main (27/11/23)
❗ Exact error message
Failed to evaluate 'theiacov_ont.assembly_fasta' (reason 1 of 1): Evaluating select_first([consensus.consensus_seq, irma.irma_assembly_fasta, ""]) failed: Cannot coerce the empty String value "" into a File.
:bug:
:pencil: Describe the Issue
When TheiaCoV_ONT is run for flu (and maybe other organisms?), if the sample does not pass the read screening, the workflow fails and no information about reasons for failure is output to the Terra table.
:repeat: How to Reproduce
:fishing_pole_and_fish: Expected Behavior
Expect for the workflow to complete successfully, but for a read screening column to be created in the Terra data table that shows that read screening has failed. This should be for flu but also for other organisms
:floppy_disk: Version Information
TheiaCoV_ONT, main (27/11/23)
❗ Exact error message
Failed to evaluate 'theiacov_ont.assembly_fasta' (reason 1 of 1): Evaluating select_first([consensus.consensus_seq, irma.irma_assembly_fasta, ""]) failed: Cannot coerce the empty String value "" into a File.