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feat: DragMap wrapper #472

Merged
merged 4 commits into from Apr 25, 2022
Merged

feat: DragMap wrapper #472

merged 4 commits into from Apr 25, 2022

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fgvieira
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@fgvieira fgvieira commented Apr 4, 2022

Description

Wrapper for Illumina's DragMap read mapper.

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 fgvieira changed the title Dragmap feat: DragMap wrapper Apr 4, 2022
@johanneskoester johanneskoester merged commit 6f54512 into snakemake:master Apr 25, 2022
@fgvieira fgvieira deleted the dragmap branch April 25, 2022 09:58
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2 participants