[COOLER] run through multiple resolutions

[nservant]

Hi

A small changes to allow to run the cload and dump cooler functions across multiple resolutions Thanks Nicolas

[nservant]

Note that I also proposed to change the channel to have always the resolution at the end to avoid the usage of map to change the order

[jianhong]

Should the test files also be changed?

[nservant]

Sorry @jianhong, I missed your message ! I'll check the test files !

[nservant]

@jianhong, I just updated the tests. However, I'm not very familiar with modules and did not yet find a way to test my changes locally ... do you know how to do it ?

[jianhong]

@jianhong, I just updated the tests. However, I'm not very familiar with modules and did not yet find a way to test my changes locally ... do you know how to do it ?

I will do that. But I need some time to finish it.

Jianhong.

[muffato]

Hi @nservant

Can you explain what you mean by "allow to run the cload and dump cooler functions across multiple resolutions" ? I don't see how that's not possible with the existing version.

[muffato]

I took a look at the tests, and there is an issue in cooler/dump. The module appends the resolution to the name of the input file, cf https://github.com/nf-core/modules/blob/ec22f9a9079bd93ff8ec152349ead5f684edeb9f/modules/cooler/dump/main.nf#L29 , which makes the path invalid and cooler complain that the file doesn't exist. I suggest removing the resolution parameter from cooler/dump altogether because it's not used at all. But then, in order to be able to chain both modules without a map, cooler/cload shouldn't output cool_bin at all either. Just meta and the cool file. How would that work for you ?

[muffato]

Hi. I actually now think it'd be easier to address these comments in #1937 since the latter contains these changes. I'll close this PR and reraise my comments over there.