Merge branch 'rework' into 'main'

Adjust to modern conventions

See merge request !1

runs/Proteomics/run.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: ProteomicsStatistics.fsx
+        entry:
+          $include: ProteomicsStatistics.fsx
+  - class: EnvVarRequirement
+    envDef:
+      - envName: DOTNET_NOLOGO
+        envValue: "true"
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [dotnet, fsi, ProteomicsStatistics.fsx]
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: "imputeKnnNoLow_35.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "imputeKnnNoLow_40.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein35zScores.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein40zScores.txt"
+
+
+arc:has technology type:
+  - class: arc:technology type
+    arc:annotation value: "Docker Container"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Benedikt"
+    arc:last name: "Venn"
+    arc:email: "venn@bio.uni-kl.de"
+    arc:affiliation: "TU Kaiserslautern"
+    arc:has role: 
+      - class: arc:role
+        arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+        arc:annotation value: "Formal analysis"
+
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

runs/Transcriptomics/run.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: TranscriptomicsStatistics.fsx
+        entry:
+          $include: TranscriptomicsStatistics.fsx
+  - class: EnvVarRequirement
+    envDef:
+      - envName: DOTNET_NOLOGO
+        envValue: "true"
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [dotnet, fsi, TranscriptomicsStatistics.fsx]
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: "2019_11_12_TPM_normalized_RNAseq_counts.csv"
+  output:
+    type: File
+    outputBinding:
+      glob: "2020_01_29_DEX_T1intercept_noCoV_multipletestingcorrected_added0_01_differencecutoff.csv"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein35zScores.txt"
+  output:
+    type: File
+    outputBinding:
+      glob: "protein40zScores.txt"
+
+
+arc:has technology type:
+  - class: arc:technology type
+    arc:annotation value: "Docker Container"
+
+arc:technology platform: ".NET"
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Benedikt"
+    arc:last name: "Venn"
+    arc:email: "venn@bio.uni-kl.de"
+    arc:affiliation: "TU Kaiserslautern"
+    arc:has role: 
+      - class: arc:role
+        arc:term accession: "https://credit.niso.org/contributor-roles/formal-analysis/"
+        arc:annotation value: "Formal analysis"
+
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl