adjust wdl to accomodate external sra fastq headers#74
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samobermiller merged 9 commits intoJun 15, 2026
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samobermiller
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Adjust
shortReadsqc.wdl, turning offfilterbytileinbbtools'rqcfilter2.shwhen the fastq has an external sra header format (@SRR/ERR/DRR). That header format is inconsistent with JGI formatting and therefore fails whenfilterbytileis enabled, as it is by default inbbtoolsv39.65, a version we will need to implement after bbtools fixes memory issue found in jaws id 168381 (no updates, original slack thread.Original failing jaws ids 168329, 168330 and 168332 from PR #63, producing threading errors when external SRA headers are parsed.
New direct jaws tests that have passed with accession ids: 184688, 184710