Add seqtk mergepe and improve docs

[mbhall88]

Description

Added

• Wrapper for seqtk mergepe
• Params section for wrapper docs
• Docs on what fields are available for use in the meta.yaml - with an example. I always have to look this up so thought it would be useful to add it to the docs
• URL field for wrapper docs (happy to remove if this isn't desirable, but it makes it more explicit that we want people to link to tool docs)
• Formatting and linting instructions in the contributing docs

Changed

• Moved contributing docs to a separate page

Removed

• Some log files that had been committed with the seqtk subsample wrappers

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,
• all environment.yaml specifications follow the respective best practices

I would usually opt for pinning the major and minor version. This way, users will get the newest security patches and bug fixes whenever they create an environment, while nothing should change in a backward incompatible way

I appreciate this may not be up for debate, in which case I'm ok to change the version, but pinning the major version only is also backward-compatible and will give all of the latest patches and fixes...

• 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,
• 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.

[jafors]

Thanks for the work. I'm a fan of the additions and restructurings in the docs.
I'd ask @johanneskoester and @dlaehnemann about their thoughts on this, but I like it. :)

[johanneskoester]

Thanks a lot! The extension of the docs looks great!! I have just a few comments below.

[dlaehnemann]

Thanks a bunch, I very much appreciate the updates to the docs. This restructuring is a very good idea. I used the opportunity to also check for consistency with our recently added PR template. So please excuse the deluge of comments and suggestions.

Regarding version pinning, I guess this is up for debate. Maybe we should debate this on Stackoverflow and adjust the wording there, if we agree to change the recommendations?

[dlaehnemann]

@mbhall88 There are still a bunch of points from my review that are open. I had to manually click on 8 hidden conversations, Load more or change over to the Files changed tab, so maybe you didn't see them in the Conversation tab of the PR?

[mbhall88]

@mbhall88 There are still a bunch of points from my review that are open. I had to manually click on 8 hidden conversations, Load more or change over to the Files changed tab, so maybe you didn't see them in the Conversation tab of the PR?

Ah very sorry @dlaehnemann. I've added those suggestions.

I think it might also be good to add a more thorough part of the docs describing how to best write a wrapper.py. I would do it, but I need to do some PhD.

[johanneskoester]

@mbhall88 There are still a bunch of points from my review that are open. I had to manually click on 8 hidden conversations, Load more or change over to the Files changed tab, so maybe you didn't see them in the Conversation tab of the PR?

Ah very sorry @dlaehnemann. I've added those suggestions.

I think it might also be good to add a more thorough part of the docs describing how to best write a wrapper.py. I would do it, but I need to do some PhD.

Thanks a lot for all your contributions although writing a thesis. This is highly appreciated!

[dlaehnemann]

@mbhall88 You're definitely right, that a detailed description of how to write a wrapper.py and wrapper.R would be great. But you're even more right to focus on your PhD. I documented that need over in the new issue #385.

Otherwise, this is good to go. I just have one suggestion for adding a sentence, but feel free to ignore that one, if you think this is not useful.

[dlaehnemann]

🎉