feat: support cloud storage URIs in CSV samplesheet path_prefix#487
Open
ikhrustalev wants to merge 2 commits into
Open
feat: support cloud storage URIs in CSV samplesheet path_prefix#487ikhrustalev wants to merge 2 commits into
ikhrustalev wants to merge 2 commits into
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Closes #484
Adds support for cloud storage URIs (
gs://,s3://, etc.) in thepath_prefixcolumn of CSV samplesheets.Problem
SamplesheetParser.resolvePath()treats any path not starting with/as relative and resolves it against the samplesheet's parent directory. Apath_prefixlikegs://bucket/path/samplegets mangled into a local path.Additionally, Nextflow's cloud path objects (e.g.
GcsPath) don't support string concatenation for suffix appending, causing downstream failures even if path resolution is fixed.Fix
gs://,s3://, etc.) via regex and return them early as plain strings, bypassing relative path resolutionTest plan
gs://path_prefix works on GCPs3://path_prefix works on AWS