I've observed this with Flu B samples, where the output FASTA file for the HA segment is an empty file. I think there's something going on with the IRMA WDL task that needs to be adjusted.
I don't think this occurs with Flu A samples, as I've seen those outputs being produced correctly from a few different labs using TheiaCoV_Illumina_PE v2.0.0
:repeat: How to Reproduce
Was this run on the Terra platform?
Terra on GCP or Azure? GCP
Or were the workflows run locally using miniwdl or cromwell?
What was the exact command was used to launch the workflow?
If possible, we may ask you to share your Terra workspace with us. Usually READER access is sufficient, but we may ask for WRITER access if we need to make changes to the workspace to reproduce the issue.
:fishing_pole_and_fish: Expected Behavior
I expect the HA segment FASTA file to include sequence and nextclade to appropriately run on this file and produce the expected nextclade outputs (aa_subs, aa_dels, clade, etc.)
:floppy_disk: Version Information
occurs on v2.0.0
:information_source: Additional Information
There are a few other known issues/optimizations to be done for IRMA and Flu-related analysis, so this fix could be coupled with those
:bug:
:pencil: Describe the Issue
I've observed this with Flu B samples, where the output FASTA file for the HA segment is an empty file. I think there's something going on with the IRMA WDL task that needs to be adjusted.
I don't think this occurs with Flu A samples, as I've seen those outputs being produced correctly from a few different labs using TheiaCoV_Illumina_PE v2.0.0
:repeat: How to Reproduce
miniwdlorcromwell?:fishing_pole_and_fish: Expected Behavior
I expect the HA segment FASTA file to include sequence and nextclade to appropriately run on this file and produce the expected nextclade outputs (aa_subs, aa_dels, clade, etc.)
:floppy_disk: Version Information
occurs on v2.0.0
:information_source: Additional Information
There are a few other known issues/optimizations to be done for IRMA and Flu-related analysis, so this fix could be coupled with those
https://github.com/theiagen/public_health_bioinformatics/issues/426
https://github.com/theiagen/public_health_bioinformatics/issues/412
https://github.com/theiagen/public_health_bioinformatics/issues/409
Along with updating to IRMA v1.1.5 docker image which is now available on dockerhub here: https://hub.docker.com/r/cdcgov/irma/tags