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fix: consensus meta wrapper #977

Merged
merged 6 commits into from Jan 20, 2023
Merged

fix: consensus meta wrapper #977

merged 6 commits into from Jan 20, 2023

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FelixMoelder
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@FelixMoelder FelixMoelder commented Jan 18, 2023

Description

Currently the snakemake meta wrapper does not transfer information defined in the fastq description field to the bam records during remapping the consensus reads.
Thereby strand information are lost in the resulting bam-file.
As a result variants called by varlociraptor do not benefit from these information.

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).

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@dlaehnemann dlaehnemann left a comment

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LGTM

@dlaehnemann dlaehnemann merged commit a320aa5 into master Jan 20, 2023
@dlaehnemann dlaehnemann deleted the fix_consensus_meta branch January 20, 2023 08:37
johanneskoester pushed a commit that referenced this pull request Jan 20, 2023
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2 participants