feat: cooltools wrappers

[Phlya]

Description

Added the first wrapper to cooltools, chose to try with cooltools insulation to see how it works.
ADD: now also added two more wrappers, will add more.

I think I did everything correctly, but it's my first time :)

QC

For all wrappers added by this PR, I made sure that

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.

[fgvieira]

Hi @Phlya, and thanks for your contributions!

Made some suggestions. If they make sense, can you also apply them on the other wrappers?

Also, does cooltools use a temp directory?

[Phlya]

Thank you for the comments @fgvieira! I'll look through them carefully.

I don't think any of the tools use a temporary directory or any temporary files, but I'll check. Does it need to be treated in a special way somehow?

[fgvieira]

If they use a temporary folder, use python's tempfile (you can check other wrappers for inspiration).

[Phlya]

I tried not specifying any dependencies in the environment and it seems to work fine! I think now this is ready for merging?

[fgvieira]

I think it looks good, apart from "range" where I hope @johanneskoester can give some input.

[Phlya]

Thank you! I could make something nicer for the range, but I think in the next version it won't be a required argument anymore, so don't want to invest too much into dealing with it.

[Phlya]

So after all I added the final wrapper that I was having problems with earlier.

[Phlya]

I removed the import where things were failing... But it shouldn't have failed anyway, that package should be installed as a dependency.

[Phlya]

Why is it failing when importing in the Snakefile?

[Phlya]

Ah I guess the environment is only activated within the execution of the rule! Oh that's tricky, is there a recommended way to circumvent that? The test data is too big to be in the repo and needs to be downloaded, and the normal way to do it is using the cooltools package...

[fgvieira]

Can you make a smaller dummy test dataset?

[Phlya]

In principle yes.

[fgvieira]

Then it should be fine for testing purposes.

[Phlya]

OK thanks, I did it.

[Phlya]

Hi, do we need @johanneskoester to approve the solution for "range"? I'd like for this to be merged soon...

[fgvieira]

Yeah, I'd like to hear his opinion on the "range" solution.
Either way, only he can make a new release.

[johanneskoester]

Sorry for being late to the party. I have a look now.

[johanneskoester]

I think this is ok.

[Phlya]

Thanks a lot @johanneskoester !