Merge branch 'deseq2' into 'main'

Deseq2

See merge request !3

runs/deseq2-run/README.md

+
+
+
+```bash
+cd runs/deseq2-run
+```
+
+```bash
+cwltool ../../workflows/deseq2/deseq2.cwl job.yml
+```

runs/deseq2-run/job.yml

+inKallistoResults:
+    class: Directory
+    path: ../../runs/kallisto/kallisto_results
+inMetadataFile:
+    class: File
+    path: ../../runs/merged_isa_metadata/out/merged_isa.tsv
+inMetadataSample: "Source.Name"
+inMetadataFactor:
+  - "Factor..Photosynthesis.mode."
\ No newline at end of file

runs/isaSampleToRawDataSeq/README.md

+
+
+
+```bash
+cd runs/isaSampleToRawDataSeq
+```
+
+```bash
+cwltool ../../workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl job.yml
+```

runs/isaSampleToRawDataSeq/job.yml

+arcPath: 
+  class: Directory
+  path: ../../
+assayName: "Talinum_RNASeq_minimal"
+outName: "rnaseq-samples"
+startingNodeNum: 1

workflows/deseq2/README.md

+# DESeq2
+
+Workflow used for **differential gene expression analysis**
+
+## DESeq2 docs
+
+- https://bioconductor.org/packages/release/bioc/html/DESeq2.html
+
+## Importing kallisto output with tximport
+
+- https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto
+
+
+## Run pure script
+
+```bash
+RScript deseq2.R "../../runs/kallisto/kallisto_results" "../../runs/merged_isa_metadata/out/merged_isa.tsv" "Source.Name" "Factor..Photosynthesis.mode."
+```
+
+## Run CWL
+

workflows/deseq2/dependencies.R

+
+# Install dependencies for deseq2
+
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("DESeq2")
+library("DESeq2")
+
+BiocManager::install("tximport")
+library("tximport")
+
+BiocManager::install("rhdf5")
+library("rhdf5")

workflows/deseq2/deseq2.R

+# DESeq2
+
+## Libraries
+
+library("DESeq2")
+library("tximport")
+library("rhdf5")
+library("ggplot2")
+
+## In-and-out
+
+inKallistoResults <- "../../runs/kallisto/kallisto_results"
+inMetadataFile <- "../../runs/merged_isa_metadata/out/merged_isa.tsv"
+inMetadataSample <- "Source.Name"
+inMetadataFactor <- "Factor..Photosynthesis.mode."
+
+### Read arguments from CLI
+
+args <- commandArgs(trailingOnly = T)
+
+inKallistoResults <- args[1]
+inMetadataFile <- args[2]
+inMetadataSample <- args[3]
+inMetadataFactor <- args[4]
+
+## Import kallisto count data
+
+files <- dir(inKallistoResults, recursive = T, full.names = T ,"abundance.h5")
+names(files) <- dir(inKallistoResults)
+
+txi <- tximport(files, type = "kallisto", txOut = TRUE)
+
+head(txi$counts)
+
+## Read sample metadata
+
+samples_metadata <- read.table(file = inMetadataFile, sep = "\t")
+
+samples <- samples_metadata[order(samples_metadata[[inMetadataSample]]), c(inMetadataSample, inMetadataFactor)]
+colnames(samples)[1:2] <- c("sampleID", "condition")
+
+rownames(samples) <- samples$sampleID
+
+## DESeq
+
+dds <- DESeqDataSetFromTximport(txi, colData = samples, design = ~ condition)
+
+dds <- DESeq(dds)
+
+## Outputs
+
+### Extract results
+
+res <- results(dds)
+write.csv(res, file = "results_stats.csv", append = FALSE, quote = TRUE)
+
+### Generate and save default plots
+
+png("results_ma-plot.png")
+  plotMA(res, ylim=c(-2,2))
+dev.off()
+
+vsd <- vst(dds, blind=FALSE)
+pcaData <- plotPCA(vsd, intgroup=c("condition"), returnData=TRUE)
+percentVar <- round(100 * attr(pcaData, "percentVar"))
+
+p2 <- ggplot(pcaData, aes(PC1, PC2, color=condition)) +
+  geom_point(size=3) +
+  xlab(paste0("PC1: ",percentVar[1],"% variance")) +
+  ylab(paste0("PC2: ",percentVar[2],"% variance")) + 
+  coord_fixed()
+
+png("results_pca-plot.png")
+  print(p2)
+dev.off()
+  
+
+
+
+

workflows/deseq2/deseq2.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+# hints:
+#   DockerRequirement:
+#     dockerPull: r-base:4.4.2
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: deseq2.R
+        entry:
+          $include: deseq2.R
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [RScript, deseq2.R]
+inputs:
+  inKallistoResults:
+    type: Directory
+    inputBinding:
+      position: 1
+  inMetadataFile:
+    type: File
+    inputBinding:
+      position: 2
+  inMetadataSample:
+    type: string
+    inputBinding:
+      position: 3
+  inMetadataFactor:
+    type: string[]
+    inputBinding:
+      position: 4
+
+outputs:
+  output:
+    type: File[]
+    outputBinding:
+      glob:
+        - "*.png"
+        - "*.csv"

workflows/deseq2/r-docker-test.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  - class: NetworkAccess
+    networkAccess: true
+  # - class: DockerRequirement
+  #   dockerPull: r-base:4.4.2
+
+baseCommand: [RScript, --help]
+
+inputs: []
+  
+outputs: []
+  
\ No newline at end of file

workflows/isaSampleToRawDataSeq/README.md

+
+
+```bash
+
+dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples
+
+```

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+  DockerRequirement:
+    dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: isaSampleToRawDataSeq.fsx
+        entry:
+          $include: isaSampleToRawDataSeq.fsx
+  - class: EnvVarRequirement
+    envDef:
+      - envName: DOTNET_NOLOGO
+        envValue: "true"
+  - class: NetworkAccess
+    networkAccess: true
+baseCommand: [dotnet, fsi, isaSampleToRawDataSeq.fsx]
+inputs:
+  arcPath:
+    type: Directory
+    inputBinding:
+      position: 1
+  assayName:
+    type: string
+    inputBinding:
+      position: 2
+  outName:
+    type: string
+    inputBinding:
+      position: 3
+  startingNodeNum:
+    type: int
+    inputBinding:
+      position: 4
+
+outputs:
+  output:
+    type: File[]
+    outputBinding:
+      glob:
+        - "*.tsv"
+        - "*.xlsx"

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

+// Pull out the full ISA process sequence (incl. all metadata) leading to the first Raw Data Node 
+
+// Dependencies
+
+#r "nuget: ARCtrl.NET, 2.0.2"
+#r "nuget: ARCtrl.QueryModel, 2.0.2"
+
+open System.IO
+open ARCtrl.NET
+open ARCtrl
+open ARCtrl.QueryModel
+
+// input parameters
+
+let args : string array = fsi.CommandLineArgs |> Array.tail
+let arcPath = args.[0]
+let assayName = args.[1]
+let startingNodeNum = args.[2] |> int
+let outName = args.[3]
+
+
+// test parameters
+let source = __SOURCE_DIRECTORY__
+let arcPath = Path.Combine(source, "../../")
+let assayName = "Talinum_RNASeq_minimal"
+let startingNodeNum = 1
+let outName = "rnaseq-samples"
+
+
+// Load ARC
+
+let arc = ARC.load(arcPath)
+
+let inv = arc.ISA.Value 
+
+// Load first data node
+
+let firstData = inv.GetAssay(assayName).FirstData
+
+// Create headers for output table
+let headers = [
+    CompositeHeader.Input IOType.Sample
+    for v in inv.ArcTables.ValuesOf firstData.[0] do
+        if v.IsCharacteristicValue then
+            CompositeHeader.Characteristic v.Category
+        elif v.IsParameterValue then
+            CompositeHeader.Parameter v.Category
+        elif v.IsFactorValue then
+            CompositeHeader.Factor v.Category
+        elif v.IsComponent then
+            CompositeHeader.Component v.Category
+        else failwithf "what the f is %O" v
+
+    CompositeHeader.Output IOType.Data
+]
+
+// Create rows
+
+let getRow (d: QNode) = 
+    [|
+
+    CompositeCell.createFreeText (inv.ArcTables.SamplesOf d).[startingNodeNum].Name
+
+    for v in inv.ArcTables.ValuesOf d do
+        if v.HasUnit then
+            CompositeCell.Unitized(v.ValueText, v.Unit)
+        else
+            CompositeCell.Term(v.Value.AsOntology())
+
+    CompositeCell.FreeText d.Name
+    
+    |]
+
+// Combine into table
+
+let t = ArcTable.init "FullTable"
+t.Headers <- ResizeArray headers
+
+for d in firstData do
+    t.AddRow (getRow d)
+
+// Small detour via workbook
+let ws = Spreadsheet.ArcTable.toFsWorksheet t
+
+let wb = new FsSpreadsheet.FsWorkbook()
+
+wb.AddWorksheet ws
+
+// Write to csv
+
+wb.ToCsvFile (outName + ".tsv", Separator = '\t')
+wb.ToXlsxFile (outName + ".xlsx")