feat: move pindel region bed files to input

[maehler]

Description

Recently I discovered that if you pass a non-existent bed file as a value for the command line parameters -j/--include or -J/--exclude in pindel, the program behaves as if empty files are being passed. Since these are supplied in params.extra, no checks are done on them.

I realise that this is not an issue with the wrapper, per se, but the pindel repo has been archived, and I think that modifying the wrapper might be a good way to catch potential mistakes.

Not sure whether my implementation is the best way to handle things, so thoughts and opinions are welcome.

QC

• I confirm that:

For all wrappers added by this PR,

• 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.
• Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

[fgvieira]

Why not just have the BED file as an input file? This way snakemake will check if the file exists.

And the prefix, if necesary, should be inferred by the wrapper, not specified in the rule's param.prefix.

[maehler]

I was thinking to have the bed files as inputs, but that more or less also makes them required, which I kind of wanted to avoid. If I recall correctly, it is possible to set an input to an empty list for it to not fail, and that could then be handled by the wrapper, but that's also kind of ugly. What do you think?

Good point about the prefix. I just followed the existing wrapper blindly. Having the prefix managed by the wrapper would be much cleaner.

[maehler]

I was thinking to have the bed files as inputs, but that more or less also makes them required, which I kind of wanted to avoid. If I recall correctly, it is possible to set an input to an empty list for it to not fail, and that could then be handled by the wrapper, but that's also kind of ugly.

Or no, I'm being a square. Whether the argument would be optional or not would be handled by the wrapper. Much cleaner.

[maehler]

@fgvieira should I open a new PR, or just modify this one?

[fgvieira]

Just modify this one...

[fgvieira]

It looks great! Just some small cosmetic suggestions. 😄

[maehler]

It looks great! Just some small cosmetic suggestions. 😄

Great, thanks for the input! This turned out a lot better.

[fgvieira]

It seems there is a conflict on test.py. Can you take a look at it?

[maehler]

Should be good to go now.