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fix if statement syntax for parsing dorado log
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kapsakcj committed Nov 18, 2024
1 parent 3a6488b commit 82a7962
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion tasks/basecalling/task_dorado_basecall.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ task basecall {

# Log the resolved model name
echo "DEBUG: Parsing model name from dorado log or capturing string from user input..."
if [ "~{dorado_model}" == "fast" || "~{dorado_model}" == "hac" || "~{dorado_model}" == "sup" ]; then
if [ "~{dorado_model}" == "fast" ] || [ "~{dorado_model}" == "hac" ] || [ "~{dorado_model}" == "sup" ]; then
echo "DEBUG: User provided either fast, hac, or sup as input for dorado_model variable, parsing log for explicit model name now..."
grep -m 1 'downloading' dorado_basecall.log | sed -e 's/.*downloading //' -e 's/ with.*//' | tr -d '\n' | tee DORADO_MODEL

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