wdl

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**The goal of `THE ARENA` is to ensure new lints produce sane warnings for WDL "in the wild".** New `--arena` flag for `wdl-gauntlet` that ignores all syntax errors (`ParseError` or...

a-frantz

Consolidate preamble comment warnings

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See an example of a "bad" preamble here: https://github.com/aws-samples/amazon-omics-tutorials/blob/main/example-workflows/gatk-best-practices/workflows/germline-fastqs-to-vcf/sub-workflows/fastq-to-ubam.wdl I'm not sure who owns this code (whether it's the Broad or Amazon), but they are using double-pound sign comments the...

a-frantz

feat: implement parsing command sections in the experimental parser.

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This commit implements parsing of command sections in tasks for the experimental parser. Before submitting this PR, please make sure: - [x] You have added a few sentences describing the...

peterhuene

This pull request adds a new rule to `wdl`. - **Rule Name**: `double_quotes` - **Rule Kind**: Lint warning - **Rule Code**: `v1::W012` - **Packages**: `wdl-grammar` Warns about strings defined with...

simojoe

feat: implement parsing of workflow statements in the experimental parser.

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This commit implements parsing of workflow statements in the experimental parser. The workflow statements include call statements, scatter statements, and conditional statements. With this, the experimental parser should now be...

peterhuene

feat: implement parsing runtime sections in the experimental parser.

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This commit implements parsing the task `runtime` section in the experimental parser. Before submitting this PR, please make sure: - [x] You have added a few sentences describing the PR...

peterhuene

In [workflows](https://github.com/stjudecloud/workflows) we have multiple variables that end in the suffix `_md5`. These get flagged by the `snake_case` rule as needing to be changed to `*_md_5`. I'd call that a...

a-frantz

negative value in `parameter_meta` parse error

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For the following `parameter_meta` entry: ``` alignSJstitchMismatchNmax: { description: "This overrides the STAR alignment default. Maximum number of mismatches for stitching of the splice junctions (-1: no limit) for: (1)...

adthrasher

feat: implements true WDL string literal parsing

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This PR introduces true WDL string literal parsing (as opposed to simply punting it and storing it as a native `String`). Before submitting this PR, please make sure: - [x]...

claymcleod

This pull request adds a new rule to `wdl`. - **Rule Name**: `literal_container_unique` - **Rule Kind**: Lint warning/Validation error - **Rule Code**: `v1::W008` - **Packages**: `wdl-grammar` _Describe the rules you...

adthrasher