Add -user-secret and -workspace-secret flags to nextflow launch

[rnaidu-seqera]

Summary

nextflow launch submits jobs to Seqera Platform via the /workflow/launch API but never includes userSecrets or workspaceSecrets in the request payload. As a result, Platform has no secrets to store in AWS Secrets Manager for the run, yet the Batch job environment always has NXF_ENABLE_SECRETS=true set — causing Nextflow to attempt and fail to fetch secrets that were never stored.

This is inconsistent with a LaunchPad-initiated run, where the UI gathers secret selections from the user and includes them in the same API request. This bug was reported via the Support Team.

Changes

• Added -user-secret and -workspace-secret CLI flags to CmdLaunch (can be specified multiple times, one secret name per flag)
• Added userSecrets and workspaceSecrets fields to LaunchOptions
• Wired both fields into buildLaunchRequestPayload() in LaunchCommandImpl so they are included in the API request to Platform

Usage

nextflow launch <pipeline-repo> \
    -r main \
    -profile awsbatch \
    -workspace-secret DRAGEN_USERNAME \
    -workspace-secret DRAGEN_PASSWORD \
    -user-secret MY_USER_SECRET

Testing

Added two tests to LaunchCommandImplTest.groovy in the existing Launch Request Building Tests section:

• should include workspace and user secrets in launch request — verifies that when -user-secret / -workspace-secret values are provided, they appear in the API payload as a Set
• should not include secrets in launch request when none provided — verifies that when no secrets are specified, neither key appears in the payload at all

Related

Closes #7039

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[ewels]

LGTM, though please add some docs :)

'cc @christopher-hakkaart for visibility.

[christopher-hakkaart]

@rnaidu-seqera - I've added some minimal docs. Can you please check for accuracy?

[rnaidu-seqera]

Looks great, thanks @christopher-hakkaart!