feat: whatshap haplotag

[pdimens]

Description

Add a wrapper for whatshap haplotag, a submodule of whatshap that phases BAM files using a phased VCF file. It also initiates the framework for adding other whatshap modules.

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).

[pdimens]

@jrderuiter @johanneskoester there is a silent testing error that still lets the things pass:

 =============================== warnings summary ===============================
test.py:134
  /home/runner/work/snakemake-wrappers/snakemake-wrappers/test.py:134: SyntaxWarning: invalid escape sequence '\.'
    "for env in `conda env list | grep -P '\.snakemake/conda' | "

[fgvieira]

Remember to add a test.

[pdimens]

@fgvieira thanks for the reviews and comments. I didn't realize I had to add manual tests to test.py, so thanks for bringing that to my attention too!

[fgvieira]

Only VCF and BAM are supported, or also BCF and SAM/CRAM?
If the latter, maybe the names should be a bit more generic. For example, instead of input.bam, maybe input.aln.

[pdimens]

@fgvieira good point, let me make it more generic. The docstring specifies compressed format, so I updated the wording to reflect vcf.gz and bcf along with BAM/CRAM.

[pdimens]

@fgvieira sorry, that's my bad. The x was uppercase in the filenames and I didn't realize it 🤦

[fgvieira]

Just small small changes, since I realized that the VCF and BAM index files do not need to be named.

[pdimens]

testing failed b/c it was missing the fasta fai file. I added it and included it in the metadata and snakefile.

[pdimens]

Odd, I thought I borrowed the right files from the Whatshap repo. I'll have to investigate this tomorrow. Thanks for the ongoing assistance

[pdimens]

@fgvieira I replaced the test files with the ones from data/pacbio/ in the whatshap directory. I tested whatshap haplotag with those files locally on my system and hopefully it works this time around.

[pdimens]

should have been a filename issue. was corrected

[fgvieira]

Great work! Seems to be working now.
Will merge, if you do not have any other changes.
Thanks for your efforts..

[pdimens]

Awesome, thank you! And sorry for this not being as straightforward as it could have been. Long time listener, first time caller 😁