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[TheiaCoV_Fasta_Batch] Substitute FASTA concatenating task to ensure proper sample_id propagation #274
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…what comes in the headers input array
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This works great! One thing we might want to consider doing is removing the long Array[Pair[String, File]] object since it's no longer necessary and just passing in the array of samplenames instead. That would simply the code a bit and I think it would be worth it.
Once that's done, I'll approve & merge. Well done! ⭐
…sk and subtitute it by samplenames string array
…agen/public_health_bioinformatics into im-theiacov-fasta-batch-fix
All done! :D And thank you for finding and squishing the newline bug! 😍 |
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Closes #261
🛠️ Changes Being Made
This PR introduces a new task to concatenate FASTA files where the array of samplenames are passed along the FASTA files for correct sample_id propagation. This is important for cases where the FASTA header doesn't match the assigned sample_id, such as with GISAID FASTA files
Impacted Workflows/Tasks
TheiaCoV_FASTA_Batch
🧠 Context and Rationale
None to be considered.
📋 Workflow/Task Steps
The new
cat_files_fasta
task has been integrated onto the TheiaCoV_Fasta_Batch workflow. It is not used by any other workflows.Inputs
None added.
Outputs
No outputs were altered.
Impacted Outputs
No outputs were altered.
🧪 Testing
Underway!Locally
Terra
https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/ad02cccf-63e7-4bc6-9eb6-c4b430113260
Scenarios for Reviewer to Test
🔬 Quality checks
Pull Request (PR) checklist: