runs/RNA_OntologyEnrichment/Rna40Enrichments1vs6_dep.txt

+biodegradation of xenobiotics	7	0.031336
+cell.organisation.cytoskeleton.mikrotubuli	5	0.023171
+TCA / organic transformation.TCA	7	0.022303
+PS.carbon concentrating mechanism	10	0.017339
+nucleotide metabolism.deoxynucleotide metabolism	6	0.007552
+amino acid metabolism.synthesis.aspartate family.methionine	6	0.007552
+gluconeogenesis / glyoxylate cycle	5	0.006356
+cell wall.cell wall proteins	4	0.004989
+cell.division	17	0.004198
+cell.motility.eukaryotes.central pair	7	0.000559
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs	6	0.000199
+cell.motility.eukaryotes.flagellar associated proteins	22	0.000157
+nucleotide metabolism.phosphotransfer and pyrophosphatases	10	0.000110
+cell.motility.eukaryotes.radial spoke.stalk	7	0.000059
+cell.motility.eukaryotes.basal bodies	12	0.000030
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	8	0.000003
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A	6	0.000002
+cell.motility.eukaryotes.intraflagellar transport.IFT motor protein	6	0.000002
+cell.organisation	40	0.000001
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	9	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	8	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species	11	0.000000
+cell.motility.eukaryotes.radial spoke	10	0.000000
+protein.synthesis	65	0.000000
+protein.synthesis.ribosomal protein	40	0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B	11	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	16	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm	18	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	36	0.000000
+cell	181	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	25	0.000000
+cell.motility.eukaryotes	114	0.000000
+cell.motility	114	0.000000
+cell.motility.eukaryotes.intraflagellar transport	23	0.000000
+cell.motility.eukaryotes.axonemal dyneins.outer arm	13	-0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein	17	-0.000000
+cell.motility.eukaryotes.axonemal dyneins	31	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs6_enr.txt

+secondary metabolism.flavonoids	6	0.043749
+misc.alcohol dehydrogenases	6	0.037091
+misc.rhodanese	7	0.037091
+nucleotide metabolism.degradation	8	0.005679
+amino acid metabolism.degradation.branched chain group.shared	5	0.005599
+amino acid metabolism.degradation.branched chain group	8	0.003524
+misc	59	0.000090

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs7_dep.txt

+protein.synthesis.ribosome biogenesis	15	0.044974
+transport.calcium	6	0.043701
+cell.division	15	0.018691
+nucleotide metabolism.deoxynucleotide metabolism	6	0.006803
+gluconeogenesis / glyoxylate cycle	5	0.005672
+nucleotide metabolism	28	0.004882
+TCA / organic transformation.TCA	8	0.004882
+cell.motility.eukaryotes.basal bodies	9	0.003512
+TCA / organic transformation	12	0.002298
+cell.motility.eukaryotes.flagellar membrane proteins	5	0.001306
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	6	0.001188
+protein.synthesis.ribosomal protein	29	0.000790
+protein.synthesis	51	0.000652
+nucleotide metabolism.phosphotransfer and pyrophosphatases	9	0.000652
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs	6	0.000207
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	7	0.000056
+cell.motility.eukaryotes.central pair	8	0.000056
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	10	0.000050
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	7	0.000011
+cell.motility.eukaryotes.intraflagellar transport.IFT motor protein	6	0.000002
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A	6	0.000002
+cell.organisation	39	0.000001
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	16	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species	12	0.000000
+cell.motility.eukaryotes.radial spoke.stalk	10	0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B	10	0.000000
+cell.motility.eukaryotes.radial spoke	13	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	25	0.000000
+cell.motility.eukaryotes.flagellar associated proteins	31	0.000000
+cell	193	0.000000
+cell.motility.eukaryotes.intraflagellar transport	22	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm	21	0.000000
+cell.motility	129	0.000000
+cell.motility.eukaryotes	129	0.000000
+cell.motility.eukaryotes.axonemal dyneins	35	0.000000
+cell.motility.eukaryotes.axonemal dyneins.outer arm	14	-0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein	16	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs7_enr.txt

+misc.UDP glucosyl and glucoronyl transferases	13	0.043774
+secondary metabolism.flavonoids.dihydroflavonols	5	0.040647
+misc.gluco-, galacto- and mannosidases	9	0.039263
+misc.alcohol dehydrogenases	7	0.037587
+amino acid metabolism.degradation.branched chain group	8	0.015498
+misc.cytochrome P450	8	0.015498
+amino acid metabolism.degradation.branched chain group.shared	5	0.015471
+secondary metabolism.flavonoids	8	0.013091
+PS.carbon concentrating mechanism.algal	9	0.012365
+nucleotide metabolism.degradation	9	0.012365
+hormone metabolism	29	0.006992
+misc.misc2	16	0.004774
+misc.rhodanese	10	0.004774
+protein.degradation.autophagy	6	0.004774
+hormone metabolism.auxin	10	0.004774
+hormone metabolism.auxin.signal transduction	10	0.000219
+	1337	0.000090
+misc	100	0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs8_dep.txt

+nucleotide metabolism	29	0.031064
+nucleotide metabolism.deoxynucleotide metabolism	6	0.018008
+TCA / organic transformation.TCA	8	0.015472
+gluconeogenesis / glyoxylate cycle	5	0.013724
+TCA / organic transformation	12	0.010639
+cell.motility.eukaryotes.central pair.C1a	4	0.009915
+PS.carbon concentrating mechanism	12	0.006927
+cell.motility.eukaryotes.flagellar membrane proteins	5	0.003233
+cell wall.cell wall proteins.proline rich proteins	4	0.001029
+cell.motility.eukaryotes.basal bodies	11	0.000768
+cell wall.cell wall proteins	5	0.000739
+protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs	6	0.000574
+nucleotide metabolism.phosphotransfer and pyrophosphatases	10	0.000479
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	8	0.000011
+cell.motility.eukaryotes.intraflagellar transport.IFT motor protein	6	0.000004
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex A	6	0.000004
+cell.organisation	43	0.000002
+cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species	11	0.000002
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	9	0.000002
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	8	0.000002
+cell.motility.eukaryotes.central pair	10	0.000002
+protein.synthesis	69	0.000001
+protein.synthesis.ribosomal protein	42	0.000000
+cell.motility.eukaryotes.radial spoke	14	0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B	11	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	17	0.000000
+cell.motility.eukaryotes.radial spoke.stalk	11	0.000000
+cell.motility.eukaryotes.intraflagellar transport	23	0.000000
+cell	211	0.000000
+cell.motility.eukaryotes.axonemal dyneins.inner arm	20	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	37	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	26	0.000000
+cell.motility.eukaryotes.flagellar associated proteins	37	0.000000
+cell.motility.eukaryotes	142	-0.000000
+cell.motility	142	-0.000000
+cell.motility.eukaryotes.axonemal dyneins.outer arm	14	-0.000000
+cell.motility.eukaryotes.intraflagellar transport.IFT particle protein	17	-0.000000
+cell.motility.eukaryotes.axonemal dyneins	34	-0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs8_enr.txt

+amino acid metabolism.degradation.branched chain group	8	0.021163
+protein.degradation.ubiquitin.E3	28	0.020898
+protein.degradation.ubiquitin.E3.RING	21	0.019417
+amino acid metabolism.degradation.branched chain group.shared	5	0.018651
+lipid metabolism.glycerol metabolism	5	0.018651
+hormone metabolism.auxin	9	0.017701
+hormone metabolism	29	0.017559
+protein.degradation.ubiquitin	56	0.017301
+misc.alcohol dehydrogenases	8	0.016468
+hormone metabolism.auxin.signal transduction	8	0.011343
+misc.rhodanese	10	0.008027
+misc.UDP glucosyl and glucoronyl transferases	16	0.007493
+misc.misc2	17	0.004070
+	1410	0.002982
+nucleotide metabolism.degradation	11	0.001620
+protein.degradation	123	0.000069
+protein.degradation.autophagy	8	0.000046
+misc	107	0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs9_dep.txt

+PS.lightreaction.photosystem II.biogenesis	7	0.045718
+secondary metabolism.isoprenoids	16	0.045055
+cell wall.cell wall proteins	4	0.039744
+RNA	150	0.039744
+transport	92	0.037960
+hormone metabolism.cytokinin.signal transduction	5	0.029689
+protein.synthesis.ribosomal protein.unknown.large subunit	5	0.029689
+hormone metabolism.cytokinin	5	0.029689
+nucleotide metabolism.deoxynucleotide metabolism	7	0.029421
+PS.lightreaction.photosystem II	15	0.026238
+protein.targeting.chloroplast	10	0.024273
+nucleotide metabolism.phosphotransfer and pyrophosphatases.adenylate kinase	5	0.021708
+cell.division	22	0.016747
+tetrapyrrole synthesis.glu-tRNA synthetase	5	0.011622
+cell.organisation	42	0.009061
+PS.carbon concentrating mechanism	15	0.007435
+cell wall.cell wall proteins.proline rich proteins	4	0.007435
+tetrapyrrole synthesis.magnesium chelatase	4	0.007435
+protein.synthesis	71	0.005678
+transport.metabolite transporters at the mitochondrial membrane	16	0.001567
+cell	133	0.001567
+PS.lightreaction	38	0.001067
+nucleotide metabolism.phosphotransfer and pyrophosphatases	12	0.000594
+cell.motility.eukaryotes.basal bodies	15	0.000070
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit	9	0.000065
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar	9	0.000025
+tetrapyrrole synthesis	21	0.000025
+PS	62	0.000005
+protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit	9	0.000002
+protein.synthesis.ribosomal protein	51	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit	21	0.000000
+protein.synthesis.ribosomal protein.prokaryotic.chloroplast	30	0.000000
+protein.synthesis.ribosomal protein.prokaryotic	44	0.000000

runs/RNA_OntologyEnrichment/Rna40Enrichments1vs9_enr.txt

+amino acid metabolism.degradation.branched chain group.shared	5	0.041771
+misc	80	0.032131
+fermentation	7	0.020183
+amino acid metabolism.degradation.branched chain group	9	0.020183
+amino acid metabolism.degradation	21	0.014129
+amino acid metabolism.synthesis.histidine	9	0.000271
+protein.degradation.ubiquitin.E3.RING	28	0.000271
+amino acid metabolism	56	0.000271
+protein.degradation.ubiquitin.E3	39	0.000050
+protein.degradation.ubiquitin	75	0.000012
+protein.degradation.autophagy	9	0.000002
+protein.degradation	157	0.000000

runs/RNA_OntologyEnrichment/job.yml

+arcDirectory:
+  class: Directory
+  path: ../../
+inputFolder:
+  class: File
+  path: ../Transcriptomics/snapshots/
+outputFolder: ./
\ No newline at end of file

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