Check for import in all workflows

[LouisLeNezet]

Description of the bug

When in a main.nf file multiple workflow {} scope are present only the first one will be checked for the use of the imported process or function.
The main_nf() function should take into account all the workflows when checking the included components

Command used and terminal output

nf-core subworkflows lint nf-core_utils_.*_pipeline

System information

No response