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feat: support cloud storage URIs in CSV samplesheet path_prefix#487

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ikhrustalev wants to merge 2 commits into
PGScatalog:mainfrom
haplotypelabs:feat/cloud-uri-samplesheet
Open

feat: support cloud storage URIs in CSV samplesheet path_prefix#487
ikhrustalev wants to merge 2 commits into
PGScatalog:mainfrom
haplotypelabs:feat/cloud-uri-samplesheet

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Summary

Closes #484

Adds support for cloud storage URIs (gs://, s3://, etc.) in the path_prefix column of CSV samplesheets.

Problem

SamplesheetParser.resolvePath() treats any path not starting with / as relative and resolves it against the samplesheet's parent directory. A path_prefix like gs://bucket/path/sample gets 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

  • Detect URI schemes (gs://, s3://, etc.) via regex and return them early as plain strings, bypassing relative path resolution
  • Returning as strings (rather than Nextflow path objects) ensures suffix concatenation works correctly downstream

Test plan

  • CSV samplesheet with gs:// path_prefix works on GCP
  • CSV samplesheet with s3:// path_prefix works on AWS
  • Local relative and absolute paths still resolve correctly

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Support cloud storage URIs (gs://, s3://) in CSV samplesheets

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