Clinical-Genomics / cg / 15705343992

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fix nextflow store available (#4450)(patch)

## Description
 The CLI command `store-available` for nextflow pipelines exited before all cases were evaluating for storing. This PR makes sure that `click.abort` is invoked only after all cases have been assesed and at least one got an exception caught.

### Added

- sentinel variable that changes from True to False when an exception is caught for the store-available commands

9 of 26 new or added lines in 5 files covered. (34.62%)

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