♻️ refactor(cli): add -with-seqera and SEQERA_ACCESS_TOKEN as aliases for nextflow run #6168
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Signed-off-by: Ken Brewer <[email protected]>
…as to TOWER_ACCESS_TOKEN Signed-off-by: Ken Brewer <[email protected]>
Revert addition of SEQERA_ACCESS_TOKEN as an alias for TOWER_ACCESS_TOKEN. The code now only supports TOWER_ACCESS_TOKEN as before. - Remove SEQERA_ACCESS_TOKEN priority logic from TowerClient.getAccessToken() - Remove SEQERA_ACCESS_TOKEN priority logic from PlatformHelper.getAccessToken() - Revert error messages to only mention TOWER_ACCESS_TOKEN - Remove updated docstrings mentioning SEQERA_ACCESS_TOKEN support Signed-off-by: Ken Brewer <[email protected]>
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Documentation updates:
docs/reference/cli.mdto replace references to-with-towerwith-with-seqera, including examples, descriptions, and monitoring instructions. [1] [2] [3] [4]Code updates for CLI options:
nextflow runto support both-with-towerand-with-seqeraoptions for monitoring workflows with the Seqera Platform.Launcher.groovyto normalize arguments for the new-with-seqeraoption alongside-with-tower.Test updates:
LauncherTest.groovyto ensure the new-with-seqeraoption is processed correctly.Importantly, this PR doesn't change the
towerconfig or theTOWER_*environment variables, which could be addressed in a separate PR.It also is a non-breaking change as previous users using the
-with-towercli arg will be able to continue doing so.