Cooltools insulation

[nservant]

new modules cooltools/insulation

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[SPPearce]

Presumably the .tsv file varies every time you run it, else it would have a md5sum in the .yml, but you should be able to use contains to check for a word in it.

[SPPearce]

Bumping the PR, it looks like it is virtually ready, can we get it finished off?

Stale

[SPPearce]

@nservant, I've updated this to nf-test. I have also swapped to just a cooltools container rather than the mulled one; if this is an issue then seqera containers will be the answer once we have that fully up and running.

I think the only thing outstanding is that the test-data is using a github link, which we would like to avoid. So we'd rather use the cooler test data that already exists in the git repo (perhaps put through another tool as a setup requirement), or add some new test data. I tried swapping to the test_merge_cool file, but that gave me an error.

[famosab]

Bump :)

[SPPearce]

Bump :)

To be honest, I'm tempted to just merge this here with an external github link.

[famosab]

Bump :)

To be honest, I'm tempted to just merge this here with an external github link.

The meta.yml linting also needs to be fixed so :/

[SPPearce]

Bump :)

To be honest, I'm tempted to just merge this here with an external github link.

The meta.yml linting also needs to be fixed so :/

Eh, that is doable.

[nservant]

Hi guys, @SPPearce

cooler insulation usually requires a normalized (balanced) contact maps, which is not the case of the toy.symm.upper.2.cool dataset.
To fix it, you could run ;

cooltools insulation toy.symm.upper.2.cool --clr-weight-name '' --ignore-diags 1

Otherwise, we can add an additional normalized dataset in test ? The latest will make more sense to really test the tool, but that's not mandatory.
N

[famosab]

@nservant If its small test data I would be in favor of adding it to our own test-datasets github if there is no other suitable data available over there

[SPPearce]

Hi guys, @SPPearce

cooler insulation usually requires a normalized (balanced) contact maps, which is not the case of the toy.symm.upper.2.cool dataset. To fix it, you could run ;

cooltools insulation toy.symm.upper.2.cool --clr-weight-name '' --ignore-diags 1

Otherwise, we can add an additional normalized dataset in test ? The latest will make more sense to really test the tool, but that's not mandatory. N

So we can use the same tool to make a correct input for this one? We could just do that inside the nf-test then.

[SPPearce]

Can you please add ontologies to the meta.yml file (https://nf-co.re/blog/2025/modules-ontology)

[Thibault-Poinsignon]

Hello @SPPearce, I updated the edam ontologies and did the other corrections. I couldn't find an ontology for .cool files, does it exist?

[SPPearce]

Hello @SPPearce, I updated the edam ontologies and did the other corrections. I couldn't find an ontology for .cool files, does it exist?

Absolutely no idea, I don't know anything about the ontologies, some other people care more than me about this. The way to add things seems to be detailed here .
I'm not going to block the PR without this.