T54A refactoring

[bclenet]

This Pull Request is related to issue #76.

Changes proposed in this Pull Request:

• Refactoring of pipeline T54A so that it conforms with the narps_open.runner module.
• Writing tests for pipeline T54A (cf. issue [TEST] Create pipeline tests #53)

Checklist:

• Descriptive title
• Targets the main branch
• Changes are functional
• My code is explicit and comments were added to it
• Code conforms with PEP8
• Tests were added for the changes and they complete successfully
• Existing tests were updated (if needed) and they complete successfully
• Documentation was updated

[cmaumet]

Discussed on January 23, current issue: cope and varcope are not generated as outputs of the run levels (and then the first level fails)