towards wrap deseq in cwl

runs/deseq2/README.md

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

runs/deseq2/job.yml

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

workflows/deseq2/README.md

@@ -9,3 +9,14 @@ Workflow used for **differential gene expression analysis**
 ## 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/deseq2.R

+# DESeq2
+
+## Libraries
+
+library("DESeq2")
+library("tximport")
+library("rhdf5")
+library("ggplot2")
+
+## In-and-out
+
+# arcPath <- "../../"
+# 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)
+
+arcPath <- args[1]
+inKallistoResults <- args[2]
+inMetadataFile <- args[3]
+inMetadataSample <- args[4]
+inMetadataFactor <- args[5]
+
+## Import kallisto count data
+
+files <- dir(file.path(arcPath, inKallistoResults) , recursive = T, full.names = T ,"abundance.h5")
+names(files) <- dir(file.path(arcPath, inKallistoResults))
+
+txi <- tximport(files, type = "kallisto", txOut = TRUE)
+
+head(txi$counts)
+
+## Read sample metadata
+
+samples_metadata <- read.table(file = file.path(arcPath, inMetadataFile), sep = "\t")
+
+samples <- samples_metadata[order(samples_metadata[[inMetadataSample]]), c(inMetadataSample, inMetadataFactor)]
+colnames(samples)[1:2] <- c("sampleID", "condition")
+
+rownames(samples) <- samples$sampleID
+
+## DESeq
+
+dds <- DESeqDataSetFromTximport(txi, colData = samples, design = ~ condition)
+
+dds <- DESeq(dds)
+
+## Extract results
+
+res <- results(dds)
+res
+
+## Outputs
+
+### Generate and save default plots
+
+png("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("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:
+  arcPath:
+    type: string
+    inputBinding:
+      position: 1
+  inKallistoResults:
+    type: string
+    inputBinding:
+      position: 2
+  inMetadataFile:
+    type: string
+    inputBinding:
+      position: 3
+  inMetadataSample:
+    type: string
+    inputBinding:
+      position: 4
+  inMetadataFactor:
+    type: string[]
+    inputBinding:
+      position: 5
+
+outputs:
+  output:
+    type: File[]
+    outputBinding:
+      glob:
+        - "*"

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

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl

@@ -6,16 +6,16 @@ hints:
 requirements:
   - class: InitialWorkDirRequirement
     listing:
-      - entryname: isa-sampleToRawDataSeq.fsx
+      - entryname: isaSampleToRawDataSeq.fsx
         entry:
-          $include: isa-sampleToRawDataSeq.fsx
+          $include: isaSampleToRawDataSeq.fsx
   - class: EnvVarRequirement
     envDef:
       - envName: DOTNET_NOLOGO
         envValue: "true"
   - class: NetworkAccess
     networkAccess: true
-baseCommand: [dotnet, fsi, isa-sampleToRawDataSeq.fsx]
+baseCommand: [dotnet, fsi, isaSampleToRawDataSeq.fsx]
 inputs:
   arcPath:
     type: Directory

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

@@ -3,15 +3,13 @@
 // Dependencies
 
 #r "nuget: ARCtrl.NET, 2.0.2"
-#r "nuget: ARCtrl.QueryModel, 1.0.5"
-#r "nuget: FsSpreadsheet.CsvIO, 6.2.0"
+#r "nuget: ARCtrl.QueryModel, 2.0.2"
 
-open FsSpreadsheet.CsvIO
+// open FsSpreadsheet.CsvIO
 open FsSpreadsheet.Net
 open System.IO
 open ARCtrl.NET
 open ARCtrl
-open ARCtrl.ISA
 open ARCtrl.QueryModel
 
 // input parameters