README.md

+# ArcPrototype
 
+A prototypic ARC that implements all specification standards accordingly
\ No newline at end of file

runs/ARCMountResult/run.cwl

+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  arcDirectory: Directory
+
+steps:
+  ARCMount:
+    run: ../../workflows/ARCMount/workflow.cwl
+    in:
+      arcDirectory: arcDirectory
+    out: [output]
+
+outputs:
+  ARCMountResult:
+    type: File
+    outputSource: ARCMount/output
\ No newline at end of file

runs/ARCMountResult/run.yml

+arcDirectory:
+  class: Directory
+  path: ../../
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "ottj@rptu.de"
+    arc:affiliation: "RPTU Kaiserslautern/Landau"
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

runs/DevcontainerResult/result.csv

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runs/DevcontainerResult/run.cwl

+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  arcDirectory: Directory
+
+steps:
+  Devcontainer:
+    run: ../../workflows/Devcontainer/workflow.cwl
+    in:
+      arcDirectory: arcDirectory
+    out: [output]
+
+outputs:
+  DevcontainerResult:
+    type: File
+    outputSource: Devcontainer/output
\ No newline at end of file

runs/DevcontainerResult/run.yml

+arcDirectory:
+  class: Directory
+  path: ../../
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "ottj@rptu.de"
+    arc:affiliation: "RPTU Kaiserslautern/Landau"
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

runs/FixedScriptResult/result.csv

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runs/FixedScriptResult/run.cwl

+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  firstArg: File
+  secondArg: string
+
+steps:
+  FixedScript:
+    run: ../../workflows/FixedScript/workflow.cwl
+    in:
+      firstArg: firstArg
+      secondArg: secondArg
+    out: [output]
+
+outputs:
+  FixedScriptResult:
+    type: File
+    outputSource: FixedScript/output
\ No newline at end of file

runs/FSharpArcCapsule.yml → runs/FixedScriptResult/run.yml

-arcDirectory:
-  class: Directory
-  path: ../
 firstArg:
   class: File
-  path: ../assays/measurement1/dataset/table.csv
+  path: ../../assays/measurement1/dataset/proteomics_result.csv
 secondArg: ./result.csv
 
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "caroline.ott@rptu.de"
+    arc:affiliation: "Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau"
+
 arc:has process sequence:
-  - class: arc:process sequence
+  - class: arc:process
     arc:has input: 
       - class: arc:data
         arc:name: "./arc/assays/measurement1/dataset/table.csv"
     arc:has output:
       - class: arc:data
-        arc:name: "./arc/runs/fsResult1/result.csv"
+        arc:name: "./arc/runs/ARCMountResult/result.csv"
 
 $namespaces:
   arc: https://github.com/nfdi4plants/ARC_ontology

runs/README.md

+# CWL examples
+
+:bulb: Requires installation of a CWL runner and docker  
+→ checkout CWL guides in the [DataPLANT Knowledge Base](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/guides/arc-cwl/)
+
+All three workflow examples below (re)create the file [*/result.csv](ARCMountResult/result.csv).
+
+## with a docker container and a fixed script
+
+```bash
+cd runs/FixedScriptResult
+cwltool run.cwl run.yml
+```
+
+## With a fixed script in a mounted arc
+
+```bash
+cd runs/ARCMountResult
+cwltool run.cwl run.yml
+```
+
+## Within an ARC with a devcontainer
+
+```bash
+cd runs/DevContainerResult
+cwltool run.cwl run.yml
+```