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StaPH-B / titan

Public health bioinformatics repository for WDL workflows to analyze viral genomes.
GNU Affero General Public License v3.0
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Switch task code blocks from {} to <<< >>> #4

Closed k-florek closed 2 years ago

k-florek commented 3 years ago

This allows for easier usage of interpolating variables in bash script syntax.

jvhagey commented 3 years ago

Just to add some more details:

Switch from {} to <<<>>> syntax in the command section of both tasks and workflows to avoid bash issues. See the wdl documentation for more details.

Bash variables should have ${variable} syntax while other wdl variables should use ~{variable} syntax.

Comment to confirm which tasks and workflows have been checked. Priority should be on titan_illumina_pe.wdl