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feat: add datavzrd wrapper #535

Merged
merged 11 commits into from Aug 18, 2022
Merged

feat: add datavzrd wrapper #535

merged 11 commits into from Aug 18, 2022

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FelixMoelder
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@FelixMoelder FelixMoelder commented Aug 12, 2022

Description

A wrapper for datavzrd

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.

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@johanneskoester johanneskoester left a comment

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Some small suggestions below.

utils/datavzrd/wrapper.py Show resolved Hide resolved
utils/datavzrd/environment.yaml Show resolved Hide resolved
utils/datavzrd/meta.yaml Outdated Show resolved Hide resolved
utils/datavzrd/test/Snakefile Outdated Show resolved Hide resolved
FelixMoelder and others added 5 commits August 17, 2022 06:59
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
@johanneskoester johanneskoester merged commit 8c05064 into master Aug 18, 2022
@johanneskoester johanneskoester deleted the datavzrd branch August 18, 2022 06:41
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3 participants