Skip to content

use Nextflow.file() instead of java.io.File for samples/accessions to support cloud storage paths - #1

Open
rwilliams wants to merge 1 commit into
bactopia:mainfrom
rwilliams:fix/samples-cloud-storage-path
Open

rwilliams wants to merge 1 commit into
bactopia:mainfrom
rwilliams:fix/samples-cloud-storage-path

Conversation

@rwilliams

Copy link
Copy Markdown

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

… 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.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant