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fix: use glob for parse_kraken2_reads output to avoid interpolation issues
The output declaration File read_taxonomy = "~{out_compressed}" was failing to register on some backends. Switch to glob("*.read_taxonomy.tsv.zst")[0] which finds the file regardless of how interpolation evaluates.
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pipes/WDL/tasks/tasks_metagenomics.wdl

Lines changed: 1 addition & 1 deletion
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@@ -2189,7 +2189,7 @@ task parse_kraken2_reads {
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>>>
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output {
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File read_taxonomy = "~{out_compressed}"
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File read_taxonomy = glob("*.read_taxonomy.tsv.zst")[0]
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}
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runtime {

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