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Update wdlconfig.qmd: smoorthi edits continued #24

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Mar 29, 2024
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Update wdlconfig.qmd: smoorthi edits continued #24

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Update wdlconfig.qmd: smoorthi edits continued
sitapriyamoorthi Mar 11, 2024
542aaa6
Catching up with main and resolving merge conflicts
tefirman Mar 28, 2024
b95181c
Keeping WDL header names consistent
tefirman Mar 28, 2024
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4 changes: 3 additions & 1 deletion wdlconfig.qmd
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Expand Up @@ -19,12 +19,14 @@ This WILDS WDL configuration guide was inspired by the [BioWDL](https://biowdl.g
## Structural Guidelines

- [Structs](https://github.com/getwilds/fastq-to-cram/blob/489ccdf0697ab902ca6f775b8e51d4f0603c0c01/fastq-to-cram.wdl#L5) should be at the top of the WDL script, followed by the [workflow](https://github.com/getwilds/fastq-to-cram/blob/489ccdf0697ab902ca6f775b8e51d4f0603c0c01/fastq-to-cram.wdl#L21) itself, followed by all of its corresponding [tasks](https://github.com/getwilds/fastq-to-cram/blob/489ccdf0697ab902ca6f775b8e51d4f0603c0c01/fastq-to-cram.wdl#L80).
- While any order is technically allowed, we recommend this arrangement to promote consistency and improve readability.
- Tasks should be broken down into as small of operations as possible.
- If a task uses more than one or two command line tools, it should probably be broken up into individual tasks.
- If a task uses more than two command line tools, it should probably be broken up into individual tasks.
- [Docker containers](https://hutchdatascience.org/WDL_Workflows_Guide/the-first-task.html#docker-images-and-containers) should be assigned to every task to ensure uniform execution, regardless of local context.
- Outside of very basic images from very trusted sources, Docker images should be pulled directly from [WILDS' Docker Library](https://github.com/getwilds/wilds-docker-library) whenever possible.
- If you think a particular tool should be added to that library, [submit an issue](https://github.com/getwilds/wilds-docker-library/issues) or email us at [email protected].
- In general, [runtime attributes](https://hutchdatascience.org/WDL_Workflows_Guide/the-first-task.html#runtime-attributes) should be defined whenever possible in order to enable execution on as many [backends](https://hutchdatascience.org/WDL_Workflows_Guide/appendix-backends-and-executors.html) as possible.
- Some runtime attributes will be ignored/required based on the backend/WDL engine being used to run your workflow. Refer to the [WDL 101 guide](https://hutchdatascience.org/WDL_Workflows_Guide/appendix-backends-and-executors.html#commonly-used-runtime-attributes) for more details.

## Stylistic Guidelines

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