From c4f426712847ad0785ee4f453a5a8dba6d821884 Mon Sep 17 00:00:00 2001
From: Joott <jonathan.ott1994@gmail.com>
Date: Thu, 1 Feb 2024 20:04:26 +0100
Subject: [PATCH] add different cwl use cases
---
runs/FSharpArcCapsule.yml | 4 +++
workflows/.gitkeep | 0
workflows/FSharpArcCapsule.cwl | 29 -------------------
.../.config/dotnet-tools.json | 5 ----
.../.devcontainer/devcontainer.json | 15 ----------
.../.devcontainer/settings.vscode.json | 3 --
workflows/FSharpArcCapsule/Dockerfile | 10 -------
workflows/FSharpArcCapsule/script.fsx | 20 -------------
8 files changed, 4 insertions(+), 82 deletions(-)
delete mode 100644 workflows/.gitkeep
delete mode 100644 workflows/FSharpArcCapsule.cwl
delete mode 100644 workflows/FSharpArcCapsule/.config/dotnet-tools.json
delete mode 100644 workflows/FSharpArcCapsule/.devcontainer/devcontainer.json
delete mode 100644 workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json
delete mode 100644 workflows/FSharpArcCapsule/Dockerfile
delete mode 100644 workflows/FSharpArcCapsule/script.fsx
diff --git a/runs/FSharpArcCapsule.yml b/runs/FSharpArcCapsule.yml
index 6ecc43b..8ee0ab0 100644
--- a/runs/FSharpArcCapsule.yml
+++ b/runs/FSharpArcCapsule.yml
@@ -1,3 +1,7 @@
arcDirectory:
class: Directory
path: ../
+firstArg:
+ class: File
+ path: ../assays/measurement1/dataset/table.csv
+secondArg: ./result.csv
diff --git a/workflows/.gitkeep b/workflows/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/workflows/FSharpArcCapsule.cwl b/workflows/FSharpArcCapsule.cwl
deleted file mode 100644
index f3aa1c3..0000000
--- a/workflows/FSharpArcCapsule.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-cwlVersion: v1.2
-class: CommandLineTool
-hints:
- DockerRequirement:
- dockerImageId: "devcontainer"
- dockerFile: {$include: "FSharpArcCapsule/Dockerfile"}
-requirements:
- - class: InitialWorkDirRequirement
- listing:
- - entryname: arc
- entry: $(inputs.arcDirectory)
- writable: true
- - class: EnvVarRequirement
- envDef:
- - envName: DOTNET_NOLOGO
- envValue: "true"
- - envName: CWL
- envValue: "true"
- - class: NetworkAccess
- networkAccess: true
-baseCommand: [dotnet, fsi, "./arc/workflows/FSharpArcCapsule/script.fsx"]
-inputs:
- arcDirectory:
- type: Directory
-outputs:
- output:
- type: File
- outputBinding:
- glob: "./arc/runs/fsResult1/result.csv"
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/.config/dotnet-tools.json b/workflows/FSharpArcCapsule/.config/dotnet-tools.json
deleted file mode 100644
index b0e38ab..0000000
--- a/workflows/FSharpArcCapsule/.config/dotnet-tools.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
- "version": 1,
- "isRoot": true,
- "tools": {}
-}
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/.devcontainer/devcontainer.json b/workflows/FSharpArcCapsule/.devcontainer/devcontainer.json
deleted file mode 100644
index 71ac9e7..0000000
--- a/workflows/FSharpArcCapsule/.devcontainer/devcontainer.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "name": "F#ARC-Capsule",
- "dockerFile": "../Dockerfile",
- "appPort": [8080],
- "extensions": [
- "ionide.ionide-fsharp",
- "ms-vscode.csharp",
- "editorconfig.editorconfig",
- "ionide.ionide-paket",
- "ionide.ionide-fake"
- ],
- "mounts": [
- "source=${localWorkspaceFolder}/../../,target=/arc,type=bind,consistency=cached"
- ]
-}
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json b/workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json
deleted file mode 100644
index 5b238fa..0000000
--- a/workflows/FSharpArcCapsule/.devcontainer/settings.vscode.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "FSharp.fsacRuntime":"netcore"
-}
\ No newline at end of file
diff --git a/workflows/FSharpArcCapsule/Dockerfile b/workflows/FSharpArcCapsule/Dockerfile
deleted file mode 100644
index 982b4cd..0000000
--- a/workflows/FSharpArcCapsule/Dockerfile
+++ /dev/null
@@ -1,10 +0,0 @@
-#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
-
diff --git a/workflows/FSharpArcCapsule/script.fsx b/workflows/FSharpArcCapsule/script.fsx
deleted file mode 100644
index 155693f..0000000
--- a/workflows/FSharpArcCapsule/script.fsx
+++ /dev/null
@@ -1,20 +0,0 @@
-#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)
\ No newline at end of file
--
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