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use Nextflow.file() instead of new File() for samples/accessions to support cloud storage paths - #1
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… support cloud storage paths new File() doesn't understand s3:// (or gs://) URIs and mangles them (s3:// -> s3:/) when Java normalizes the path, causing "No such file or directory" errors on cloud-hosted samplesheets/accession files.
rwilliams
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yo! Meant to get this merged a while ago, haha but figured you probably edited things to work on your system! I'll get this merged, thank you very much for taking the time to get this figured out! |
rpetit3
approved these changes
Oct 9, 2026
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new File() doesn't understand s3:// (or gs://) URIs and mangles them (s3:// -> s3:/) when Java normalizes the path, causing "No such file or directory" errors on cloud-hosted samplesheets/accession files.
See bactopia/bactopia#679