Compare revisions

Heinrich Lukas Weil · Kevin Schneider · Heinrich Lukas Weil · Heinrich Lukas Weil · Caroline Ott · Caroline Ott
--- a/README.md
+++ b/README.md
+# ArcPrototype

+A prototypic ARC that implements all specification standards accordingly
\ No newline at end of file
--- a/assays/measurement1/isa.assay.xlsx
+++ b/assays/measurement1/isa.assay.xlsx
--- a/assays/measurement1/isa.datamap.xlsx
+++ b/assays/measurement1/isa.datamap.xlsx
--- a/assays/measurement1/isa.dataset.xlsx
+++ b/assays/measurement1/isa.dataset.xlsx
--- a/assays/measurement2/isa.assay.xlsx
+++ b/assays/measurement2/isa.assay.xlsx
--- a/isa.investigation.xlsx
+++ b/isa.investigation.xlsx
--- a/runs/fsResult1/result.csv
+++ b/runs/fsResult1/result.csv
--- a/runs/ARCMountResult/run.cwl
+++ b/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
--- a/runs/FSharpArcCapsule.yml
+++ b/runs/FSharpArcCapsule.yml
 arcDirectory:
  class: Directory
-  path: ../
-firstArg:
-  class: File
-  path: ../assays/measurement1/dataset/table.csv
-secondArg: ./result.csv
+  path: ../../

-arc:has process sequence:
-  - class: arc:process sequence
-    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: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

--- a/runs/DevcontainerResult/result.csv
+++ b/runs/DevcontainerResult/result.csv
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--- a/runs/DevcontainerResult/run.cwl
+++ b/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
--- a/runs/DevcontainerResult/run.yml
+++ b/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
--- a/runs/FixedScriptResult/isa.run.xlsx
+++ b/runs/FixedScriptResult/isa.run.xlsx
--- a/runs/FixedScriptResult/result.csv
+++ b/runs/FixedScriptResult/result.csv
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--- a/runs/FixedScriptResult/run.cwl
+++ b/runs/FixedScriptResult/run.cwl
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  - class: 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
--- a/runs/FixedScriptResult/run.yml
+++ b/runs/FixedScriptResult/run.yml
+firstArg:
+  class: File
+  path: ../../assays/measurement1/dataset/proteomics_result.csv
+secondArg: ./result.csv
--- a/runs/README.md
+++ b/runs/README.md
 # CWL examples

 :bulb: Requires installation of a CWL runner and docker  
-&rarr; checkout CWL guides in the [DataPLANT Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/guides/ComputationalWorkflows/index.html)
+&rarr; 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 [fsResult1/result.csv](fsResult1/result.csv).
+All three workflow examples below (re)create the file [*/result.csv](ARCMountResult/result.csv).

-## with a docker container
+## with a docker container and a fixed script

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/FixedScript/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/FixedScriptResult
+cwltool run.cwl run.yml
 ```

 ## With a fixed script in a mounted arc

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/ARCMount/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/ARCMountResult
+cwltool run.cwl run.yml
 ```

 ## Within an ARC with a devcontainer

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/Devcontainer/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/DevContainerResult
+cwltool run.cwl run.yml
 ```
--- a/studies/experiment1_material/README.md
+++ b/studies/experiment1_material/README.md
--- a/studies/MaterialPreparation/isa.study.xlsx
+++ b/studies/MaterialPreparation/isa.study.xlsx
--- a/studies/experiment1_material/isa.study_unnecessarilyFilled.xlsx
+++ b/studies/experiment1_material/isa.study_unnecessarilyFilled.xlsx
No results found