Clone/Pull submodules recursively

[pachiras]

Hello,

I found run command fails to download the codes of submodule of submodule (the grand daughter module) from the repository. pull and clone commands even fail to download the codes of submodule (the daughter module).

For most of the nextflow users need the submodules downloaded recursively when they run their scripts. So this is my attempt to achieve it.

version 20.05.0-SNAPSHOT build 5335
created 10-05-2020 21:32 UTC (11-05-2020 06:32 JDT)

[pachiras]

Hi, Paolo,

I have added -recurse-submodules options to run/clone/pull sub commands, as the git command does. Nextflow's behaviors on those commands should not be affected without the option. Please consider about it.

[pditommaso]

This looks doable, however currently submodules are controlled via the config file setting the attribute manifest.submodule.

For consistency, I would suggest adding recurseSubmodule. The new feature would be enabled setting

manifest {
  submodule=true
  recurseSubmodules=true
}

Would that work for you?

[pachiras]

Thank you for your comment, Paolo.
I'll try to change the code as you said.
By the way our server crashed today. It could take some time for its recovery.
Please wait for a few days.

[pditommaso]

No hurry!

[pachiras]

Hi,

Sorry to be late, but I have changed the code to control the recursive behavior from manifest scope. I hope it is acceptable. Thanks.

[pditommaso]

Nice thanks!