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fix: use string concatenation for out_filename/out_compressed in parse_kraken2_reads
~{} interpolation in task-level declarations evaluates sample_id as empty, causing output files to be named .read_taxonomy.tsv.zst. Switch to + concatenation following the classify_virnucpro_contigs pattern.
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pipes/WDL/tasks/tasks_metagenomics.wdl

Lines changed: 2 additions & 2 deletions
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@@ -2015,8 +2015,8 @@ task parse_kraken2_reads {
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}
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}
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String out_filename = "~{sample_id}.read_taxonomy.tsv"
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String out_compressed = out_filename + ".zst"
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String out_filename = sample_id + ".read_taxonomy.tsv"
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String out_compressed = sample_id + ".read_taxonomy.tsv.zst"
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command <<<
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set -e

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