Fix Azure Batch executor scratch directory support

[adamrtalbot]

Summary

• Fix process.scratch = true failing on Azure Batch with /bin/bash: .command.sh: No such file or directory
• Fix .command.in resource file incorrectly sourced from .command.sh blob URL in AzBatchService.resourceFileUrls()

Problem

When process.scratch = true, the .command.run script creates a temporary scratch directory and cds into it before executing. However, .command.sh and other control files remain in the Azure Batch task working directory (where Azure downloaded them as resource files), so nxf_launch() fails with a "No such file or directory" error.

Both AWS Batch and Google Batch handle this by staging .command.sh as an input file. AWS re-downloads from S3 (necessary since only .command.run is bootstrapped). Google uses local filesystem copies via mounted GCS.

Fix

Azure Batch already downloads .command.sh, .command.run, and .command.in as resource files to the task working directory before execution — so re-downloading from blob storage is unnecessary.

Instead, this fix:

1. Saves the original working directory as NXF_TASK_LAUNCH_DIR in AzFileCopyStrategy.getEnvScript() — this runs before the template's cd $NXF_SCRATCH, capturing where the resource files live
2. Copies control files locally in AzFileCopyStrategy.getStageInputFilesScript() — after cd $NXF_SCRATCH, copies .command.sh, .command.run, and .command.in from the saved directory using a local cp (no network round-trip)

The generated staging block:

if [[ "${NXF_SCRATCH:-}" && "${NXF_TASK_LAUNCH_DIR:-}" && "$NXF_TASK_LAUNCH_DIR" != "$PWD" ]]; then
  cp "$NXF_TASK_LAUNCH_DIR"/.command.sh . 2>/dev/null || true
  cp "$NXF_TASK_LAUNCH_DIR"/.command.run . 2>/dev/null || true
  cp "$NXF_TASK_LAUNCH_DIR"/.command.in . 2>/dev/null || true
fi

Bonus fix

AzBatchService.resourceFileUrls() was using cmdScript (.command.sh's blob URL) as the HTTP source for the .command.in resource file, meaning Azure Batch would download .command.sh content and save it as .command.in. Fixed to use the correct .command.in blob path.

Testing

• Updated existing AzFileCopyStrategyTest assertions for the new staging and env output
• Verified with a real Azure Batch run using nextflow run hello with process.scratch = true

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