Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: add wrapper for rbt vcf_fix_iupac_alleles #1209

Open
wants to merge 6 commits into
base: master
Choose a base branch
from

Conversation

fgvieira
Copy link
Collaborator

@fgvieira fgvieira commented Apr 5, 2023

Description

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).


with tempfile.TemporaryDirectory() as tmpdir:
shell(
"(rbt vcf-fix-iupac-alleles {extra} < {snakemake.input[0]} | bcftools sort --temp-dir {tmpdir} {bcftools_opts}) {log}"
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why the sort? rbt vcf-fix-iupac-alleles does not change the order of the records.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The main idea was to allow for automatic output on any format (bcf, vcf, vcf.gz).
Since I was using it to standardize resources (known variation from ensembl), I thought that sort would be a nice-to-have (just to be sure the output was sorted) and the extra runtime would be ok since it would only be run once.

But I can also remove it (or switch to view), if you prefer to keep the wrapper more general.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Copy link
Contributor

github-actions bot commented Jan 1, 2024

This PR was marked as stale because it has been open for 6 months with no activity.

@github-actions github-actions bot added the Stale label Jan 1, 2024
@fgvieira fgvieira removed the Stale label Jan 1, 2024
Copy link
Contributor

github-actions bot commented Jul 1, 2024

This PR was marked as stale because it has been open for 6 months with no activity.

@github-actions github-actions bot added the Stale label Jul 1, 2024
@fgvieira fgvieira removed the Stale label Jul 2, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants