Medaka updates for new 10.4.1 grid chemistry #12
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WDL doesn't recognize git, so use wget to download primer schemes under commit e6ddb7c (committed 6/14/23). Can't use tag to download since there hasn't been a new release or tag in 3 years.
See if it helps with empty fasta issues
This reverts commit f9bd15a.
1. Check if the consensus file is generated 2. If so, check if < 30B (empty ~16B, succeeded ~29KB) 3. If so, call medaka with strict 4. Select first for medaka outputs
This reverts commit 9715a48.
Remove trim_barcodes parameter and variable Hardcode barcode kit, remove variable Remove rerun medaka task with --strict parameter, adjust downstream variable declarations Remove debugging vcf files output
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These changes have been merged into the develop branch and will be merged to main in the v2.2.0 PR (#17) |
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Overview
Update Medaka task for new grid 10.4.1 chemistry.
Updates
New task - exit_wdl
Known issue
Problem
See issue created in artic-network.
Solution
Check the size of the fasta file generated. If under 30B, then fail the sample. A new task, exit_wdl, was written to accomplish this.
Upstream/downstream changes needed
None :)
Changes needed on user end
None :)