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correctly embed reference in bam/cram #6594

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correctly embed reference in bam/cram #6594

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Commits on Nov 28, 2024

  1. correctly embed reference in bam/cram 

    currently minimap2's bam/cram output stores a tmp file as the reference fasta. This prevents other galaxy tools from using it as the spec expects that the stored reference is a real file. This patch simply copies existing code over to ensure the real full path to the reference is used. It won't solve all cases (e.g. when reference file is deleted) but it will solve the other cases.
    @alpapan
    alpapan authored Nov 28, 2024
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