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try fix
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Brilator committed Nov 14, 2024
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22 changes: 12 additions & 10 deletions src/content/docs/cwl/cwl-examples.md
Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,15 @@ inputs:
prefix: -i
outputs:
myFileOutput:
type: File
outputBinding:
type: File
outputBinding:
# this returns a specific file
glob: myOutput.txt
glob: myOutput.txt
myFileArrayOutput:
type: File[]
outputBinding:
# this returns all files with the extension .txt
glob: $(runtime.outdir)/*.txt
# this returns all files with the extension .txt
glob: $(runtime.outdir)/*.txt
myDirectoryOutput:
type: Directory
outputBinding:
Expand Down Expand Up @@ -91,15 +91,15 @@ inputs:
prefix: -i
outputs:
myFileOutput:
type: File
outputBinding:
type: File
outputBinding:
# this returns a specific file
glob: myOutput.txt
glob: myOutput.txt
myFileArrayOutput:
type: File[]
outputBinding:
# this returns all files with the extension .txt
glob: $(runtime.outdir)/*.txt
# this returns all files with the extension .txt
glob: $(runtime.outdir)/*.txt
myDirectoryOutput:
type: Directory
outputBinding:
Expand Down Expand Up @@ -153,6 +153,7 @@ outputs:
glob: "result.csv"
```

[Example](https://git.nfdi4plants.org/muehlhaus/ArcPrototype/-/tree/main/workflows/FixedScript)

### With a fixed script in a mounted arc
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outputBinding:
glob: "./arc/runs/myRun/result.csv"
```

The Dockerfile should only include operations that reference resources that are available online or within the baseimage. COPY operations that point to local files for
example won't work in the context of CWL. If they are necessary for the execution in the devcontainer context (e.g. configuration for editors), but not the execution of the script, they
can be prefixed with a `*` to make the execution of the operation optional.
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5 changes: 2 additions & 3 deletions src/content/docs/guides/arc-cwl-wrap-script.mdx
Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,8 @@ import { Tabs, TabItem } from '@astrojs/starlight/components';
import ViolasARCFinal from '@components/mdx/ViolasARC-final.mdx'
import Mermaid from '@components/mdx/Mermaid.astro'

Here we wrap a minimal example script into a [CWL](/nfdi4plants.knowledgebase/CWL) document. We use a python script (`heatmap.py`), that creates a heatmap file (`heatmap.svg`) based on an input table containing sugar abundance assay data (`sugar_result.csv`).
Wrappig the script in CWL makes it reusable in another ARC to generate the same type of heatmap based on another input table. For more details, checkout the [CWL](/nfdi4plants.knowledgebase/CWL)

Here we wrap a minimal example script into a [CWL](/nfdi4plants.knowledgebase/cwl) document. We use a python script (`heatmap.py`), that creates a heatmap file (`heatmap.svg`) based on an input table containing sugar abundance assay data (`sugar_result.csv`).
Wrappig the script in CWL makes it reusable in another ARC to generate the same type of heatmap based on another input table. For more details, checkout the introduction to [CWL](/nfdi4plants.knowledgebase/cwl).

## Example Data

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