runs/Proteomics/heatmap/run.cwl

+cwlVersion: v1.2
+class: Workflow
+
+requirements:  
+  - class: SubworkflowFeatureRequirement
+
+inputs:
+  arcDirectory:
+    type: Directory
+    doc: "Directory for processing ARC"
+
+  outputDirectory:
+    type: Directory
+    doc: "Directory for resulting heatmap"
+
+steps:
+  workflow:
+    run: ../../../workflows/ProteomeAnalysis/workflow.cwl
+    in:
+      arcDirectory: arcDirectory
+      outputDirectory: outputDirectory
+    out: [output]
+
+outputs:
+  output:
+    type: File
+    outputSource: workflow/output
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
+
+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"

runs/Proteomics/heatmap/run.yml

+arcDirectory:
+  class: Directory
+  path: ../../../  # → points to: ../workspaces/Ru_ChlamyHeatstress
+
+outputDirectory:
+  class: Directory
+  path: .      # → will write output into ../workspaces/Ru_ChlamyHeatstress/runs/Proteomics/heatmap
\ No newline at end of file

runs/Proteomics/heatmap/run_cwl_pipeline_command.txt

+# from current folder 
+cwltool run.cwl run.yml
\ No newline at end of file

runs/Proteomics/statistics/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/RNA_OntologyEnrichment/Rna40Enrichments1vs10_dep.txt

+redox	18	0.046572
+major CHO metabolism.degradation.starch.starch cleavage	4	0.036255
+TCA / organic transformation.TCA.pyruvate DH	4	0.027340
+secondary metabolism	18	0.023703
+protein.targeting.chloroplast	7	0.021577
+protein.assembly and cofactor ligation	6	0.019517
+amino acid metabolism.synthesis.glutamate family.arginine	5	0.017260
+redox.misc	5	0.017260
+protein.aa activation	14	0.016326
+signalling.phosphinositides.phosphatidylinositol-4-phosphate 5-kinase	4	0.016168
+cell.cycle.peptidylprolyl isomerase	9	0.012316
+cell.motility.eukaryotes.flagellar membrane proteins	4	0.010644
+nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase	4	0.010644
+PS.calvin cycle.rubisco interacting	4	0.010644
+OPP	6	0.010644
+lipid metabolism	32	0.005106
+PS.lightreaction.other electron carrier (ox/red)	5	0.005099
+PS.lightreaction.unspecified	10	0.004672
+protein.synthesis	48	0.003846
+secondary metabolism.isoprenoids.carotenoids	8	0.002788
+PS.lightreaction.photosystem II.biogenesis	7	0.002023
+PS.lightreaction.cytochrome b6/f	4	0.002010
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A	4	0.002010
+secondary metabolism.isoprenoids.non-mevalonate pathway	6	0.001055
+protein.folding.immunophilins (IMM)	13	0.000788
+protein.folding.immunophilins (IMM).FKBPs	8	0.000708
+tetrapyrrole synthesis.glu-tRNA synthetase	5	0.000649
+tetrapyrrole synthesis.magnesium chelatase	4	0.000460
+cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species	8	0.000346
+secondary metabolism.isoprenoids	16	0.000262
+lipid metabolism.FA synthesis and FA elongation.acetyl CoA carboxylation	6	0.000190
+cell.motility.eukaryotes.central pair	8	0.000051
+PS.lightreaction.ATP synthase	6	0.000031
+PS.lightreaction.photosystem II.LHC-II	8	0.000014
+nucleotide metabolism.phosphotransfer and pyrophosphatases	11	0.000013
+cell.motility.eukaryotes.radial spoke	9	0.000004
+cell.motility.eukaryotes.radial spoke.stalk	8	0.000003
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	8	0.000003
+cell.motility.eukaryotes.axonemal dyneins.outer arm	10	0.000001
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	8	0.000000
+PS.lightreaction.photosystem I.LHC-I	9	0.000000
+PS.lightreaction.photosystem II.PSII polypeptide subunits	12	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	10	0.000000
+lipid metabolism.FA synthesis and FA elongation	22	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm	16	0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B	10	0.000000
+cell.motility.eukaryotes.flagellar associated proteins	31	0.000000
+PS.lightreaction	77	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	18	0.000000
+protein.synthesis.ribosomal protein	42	0.000000
+cell.motility.eukaryotes.intraflagellar transport	17	0.000000
+PS.lightreaction.photosystem I.PSI polypeptide subunits	9	0.000000
+PS.lightreaction.photosystem II	28	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	28	0.000000
+cell.motility.eukaryotes	103	0.000000
+cell.motility	103	0.000000
+cell	129	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	38	0.000000
+PS	104	0.000000
+cell.motility.eukaryotes.axonemal dyneins	26	-0.000000
+PS.lightreaction.photosystem I	18	-0.000000
+tetrapyrrole synthesis	30	-0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein	14	-0.000000
+PS.calvin cycle	16	-0.000000