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docs: Update workflow syntax with priority directive #2188

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merged 1 commit into from Apr 28, 2023
Merged

docs: Update workflow syntax with priority directive #2188

merged 1 commit into from Apr 28, 2023

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bentyeh
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@bentyeh bentyeh commented Mar 22, 2023

Description

  1. Add priority directive to Snakefile syntax specification (see https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html)
  2. Add Wikipedia link for extended Backus-Naur form (EBNF).

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

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sonarcloud bot commented Mar 22, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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@bentyeh
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bentyeh commented Mar 22, 2023

There are actually many directives that are supported by Snakemake but not currently included in the Snakefile syntax specification documentation: ruleorder, localrules, onsuccess, onerror, onstart, etc.

Unfortunately, I'm not sufficiently familiar with Snakemake to know all the supported directives. Would @johanneskoester or another more senior contributor be able to complete the syntax specification documentation with all supported directives?

Finally, perhaps it would be helpful to new users to define what the word "directive" means. The current documentation seems to use "directive" to refer to any keyword that is followed by a colon in a Snakefile. Is that accurate?

@johanneskoester johanneskoester merged commit af10db5 into snakemake:main Apr 28, 2023
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@johanneskoester
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There are actually many directives that are supported by Snakemake but not currently included in the Snakefile syntax specification documentation: ruleorder, localrules, onsuccess, onerror, onstart, etc.

Unfortunately, I'm not sufficiently familiar with Snakemake to know all the supported directives. Would @johanneskoester or another more senior contributor be able to complete the syntax specification documentation with all supported directives?

Finally, perhaps it would be helpful to new users to define what the word "directive" means. The current documentation seems to use "directive" to refer to any keyword that is followed by a colon in a Snakefile. Is that accurate?

Yes, that is correct. And indeed, the EBNF should be updated. I hope to find time for that soon.

johanneskoester pushed a commit that referenced this pull request Apr 28, 2023
🤖 I have created a release *beep* *boop*
---


##
[7.25.2](v7.25.1...v7.25.2)
(2023-04-28)


### Bug Fixes

* Fix inconsistencies between detailed summary and normal summary
([#2218](#2218))
([d903123](d903123))
* Fix race condition when creating lock directory
([#2225](#2225))
([66ea4d1](66ea4d1))
* quote paths given to singularity in order to ensure that it does not
fail when paths contain whitespace
([#2190](#2190))
([a572fb7](a572fb7))


### Documentation

* added changelog info for >v7.19.1 parsing error of "hh:mm:ss" time
format in runtime resource
([#2189](#2189))
([2889f38](2889f38))
* update misc/vim/Readme with info for packer.nvim
([#2095](#2095))
([32166a7](32166a7))
* Update workflow syntax with priority directive
([#2188](#2188))
([af10db5](af10db5))

---
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Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@bentyeh bentyeh deleted the patch-4 branch April 28, 2023 16:46
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bentyeh commented May 1, 2023

Referencing related open issues #1502 #1168 #2224

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2 participants