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Commit c4f42671 authored by Joott's avatar Joott
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add different cwl use cases

parent 33b94f72
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1 merge request!3Added cwl examples
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arcDirectory:
class: Directory
path: ../
firstArg:
class: File
path: ../assays/measurement1/dataset/table.csv
secondArg: ./result.csv
cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
dockerImageId: "devcontainer"
dockerFile: {$include: "FSharpArcCapsule/Dockerfile"}
requirements:
- class: InitialWorkDirRequirement
listing:
- entryname: arc
entry: $(inputs.arcDirectory)
writable: true
- class: EnvVarRequirement
envDef:
- envName: DOTNET_NOLOGO
envValue: "true"
- envName: CWL
envValue: "true"
- class: NetworkAccess
networkAccess: true
baseCommand: [dotnet, fsi, "./arc/workflows/FSharpArcCapsule/script.fsx"]
inputs:
arcDirectory:
type: Directory
outputs:
output:
type: File
outputBinding:
glob: "./arc/runs/fsResult1/result.csv"
\ No newline at end of file
{
"version": 1,
"isRoot": true,
"tools": {}
}
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{
"name": "F#ARC-Capsule",
"dockerFile": "../Dockerfile",
"appPort": [8080],
"extensions": [
"ionide.ionide-fsharp",
"ms-vscode.csharp",
"editorconfig.editorconfig",
"ionide.ionide-paket",
"ionide.ionide-fake"
],
"mounts": [
"source=${localWorkspaceFolder}/../../,target=/arc,type=bind,consistency=cached"
]
}
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{
"FSharp.fsacRuntime":"netcore"
}
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#FROM rocker/r-ver:3.4.4
FROM mcr.microsoft.com/dotnet/sdk:6.0
#FROM r-base
# Copy endpoint specific user settings into container to specify
# .NET Core should be used as the runtime.
COPY *.devcontainer/settings.vscode.json /root/.vscode-remote/data/Machine/settings.json
# Install git, process tools
RUN apt-get update && apt-get -y install git procps
#r "nuget: FSharp.Data, 5.0.2"
open FSharp.Data
open System.IO
printfn "%A" (System.IO.Directory.GetCurrentDirectory())
let data =
CsvFile
.Load(Path.Combine(System.IO.Directory.GetCurrentDirectory(),"./arc/assays/measurement1/dataset/table.csv"))
.Cache()
let r =
[
yield "Sum_1-2"
for row in data.Rows do
yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
]
System.IO.File.WriteAllLines("./arc/runs/fsResult1/result.csv",r)
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