Merge branch 'fsharp-cwl' into 'main'

Fsharp cwl

See merge request !9

runs/isaSampleToRawDataSeq/README.md → runs/isaSampleToRawDataSeq-run/README.md

@@ -2,7 +2,7 @@
 
 
 ```bash
-cd runs/isaSampleToRawDataSeq
+cd runs/isaSampleToRawDataSeq-run
 ```
 
 ```bash

runs/isaSampleToRawDataSeq/job.yml → runs/isaSampleToRawDataSeq-run/job.yml

@@ -2,5 +2,5 @@ arcPath:
   class: Directory
   path: ../../
 assayName: "Talinum_RNASeq_minimal"
-outName: "rnaseq-samples"
-startingNodeNum: 1
+outName: rnaseq-samples
+startingNodeNum: 0

runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv

+Input [Sample Name],Characteristic [organism],Term Source REF (OBI:0100026),Term Accession Number (OBI:0100026),Characteristic [organism part],Term Source REF (EFO:0000635),Term Accession Number (EFO:0000635),Characteristic [plant age],Term Source REF (DPBO:0000033),Term Accession Number (DPBO:0000033),Parameter [growth day length],Term Source REF (DPBO:0000041),Term Accession Number (DPBO:0000041),Parameter [light intensity exposure],Unit,Term Source REF (PECO:0007224),Term Accession Number (PECO:0007224),Parameter [humidity day],Unit ,Term Source REF (DPBO:0000005),Term Accession Number (DPBO:0000005),Parameter [temperature day],Unit  ,Term Source REF (DPBO:0000007),Term Accession Number (DPBO:0000007),Parameter [temperature night],Unit   ,Term Source REF (DPBO:0000008),Term Accession Number (DPBO:0000008),Factor [watering exposure],Term Source REF (PECO:0007383),Term Accession Number (PECO:0007383),Factor [Timepoint],Term Source REF (NCIT:C68568),Term Accession Number (NCIT:C68568),Factor [timepoint-ZT],Term Source REF (),Term Accession Number (),Factor [Photosynthesis mode],Term Source REF () ,Term Accession Number () ,Parameter [biosource amount],Unit    ,Term Source REF (DPBO:0000013),Term Accession Number (DPBO:0000013),Parameter [extraction method],Term Source REF (DPBO:0000054),Term Accession Number (DPBO:0000054),Parameter [extraction buffer],Term Source REF (DPBO:0000050),Term Accession Number (DPBO:0000050),Parameter [extraction buffer volume],Unit     ,Term Source REF (DPBO:0000051),Term Accession Number (DPBO:0000051),Parameter [RNA quality check],Term Source REF (DPBO:0000062),Term Accession Number (DPBO:0000062),Parameter [library strategy],Term Source REF (DPBO:0000035),Term Accession Number (DPBO:0000035),Parameter [library selection],Term Source REF (DPBO:0000036),Term Accession Number (DPBO:0000036),Parameter [library layout],Term Source REF (DPBO:0000015),Term Accession Number (DPBO:0000015),Parameter [library preparation kit],Term Source REF (GENEPIO:0000085),Term Accession Number (GENEPIO:0000085),Parameter [library preparation kit version],Term Source REF (GENEPIO:0000149),Term Accession Number (GENEPIO:0000149),Parameter [adapter sequence],Term Source REF (GENEPIO:0000083),Term Accession Number (GENEPIO:0000083),Parameter [next generation sequencing instrument model],Term Source REF (DPBO:0000040),Term Accession Number (DPBO:0000040),Parameter [base-calling software],Term Source REF (DPBO:0000017),Term Accession Number (DPBO:0000017),Parameter [base-calling software version],Term Source REF (DPBO:0000018),Term Accession Number (DPBO:0000018),Parameter [Raw data file format],Term Source REF (DPBO:0000021),Term Accession Number (DPBO:0000021),Output [Data]
+CAM_01,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,80,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CAGATC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+CAM_02,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,CTTGTA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+CAM_03,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought,user-specific,,MD,user-specific,,6,user-specific,,CAM,user-specific,,93,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,AGTCAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+reC3_01,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,82,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTCCGC,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+reC3_02,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,96,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+reC3_03,Talinum fruticosum,NCBITaxon,http://purl.obolibrary.org/obo/NCBITaxon_110664,leaf,PO,https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0025034,28 days after germination,user-specific,,12 hr light / 12 hr dark,user-specific,,425,microeinstein per square meter per second,UO,https://bioregistry.io/UO:0000160,37,percent,UO,https://bioregistry.io/UO:0000187,30,degree celsius,UO,https://bioregistry.io/UO:0000027,22,degree celsius,UO,https://bioregistry.io/UO:0000027,12 days drought + 2 days rewatered,user-specific,,MD,user-specific,,6,user-specific,,reC3,user-specific,,78,milligram,UO,https://bioregistry.io/UO:0000022,Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011,user-specific,,Roboklon commercial buffers,user-specific,,300,microliter,UO,https://bioregistry.io/UO:0000101,RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano),user-specific,,RNA-seq,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000003,cDNA method,user-specific,,single-end,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000086,Illumina TruSeq RNA Sample Prep Kit,,,version 2,,,GTGAAA,,,Illumina HiSeq 2000,DPBO,http://purl.org/nfdi4plants/ontology/dpbo/DPBO_1000041,Illumina Cassava,user-specific,,v1.8.2,,,*.fastq.gz,,,DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
\ No newline at end of file

workflows/deseq2/deseq2.R

@@ -6,13 +6,14 @@ library("DESeq2")
 library("tximport")
 library("rhdf5")
 library("ggplot2")
+library("readxl")
 
 ## In-and-out
 
-# inKallistoResults <- "../../runs/kallisto/kallisto_results"
-# inMetadataFile <- "../../runs/merged_isa_metadata/out/merged_isa.tsv"
-# inMetadataSample <- "Source.Name"
-# inMetadataFactorList <- list("Factor..Photosynthesis.mode.", "Factor..Biosource.amount.")
+inKallistoResults <- "../../runs/kallisto/kallisto_results"
+inMetadataFile <- "../../runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx"
+inMetadataSample <- "Input [Source Name]"
+inMetadataFactorList <- list("Factor [Photosynthesis mode]")
 
 ### Read arguments from CLI
 
@@ -34,13 +35,18 @@ head(txi$counts)
 
 ## Read sample metadata
 
-samples_metadata <- read.table(file = inMetadataFile, sep = "\t")
+samples_metadata <- as.data.frame(read_xlsx(path = inMetadataFile))
 samples <- samples_metadata[order(samples_metadata[[inMetadataSample]]), c(inMetadataSample, unlist(inMetadataFactorList))]
+
 rownames(samples) <- samples[,inMetadataSample]
 
 factors <- sapply(inMetadataFactorList, function(x) x[[1]])
-design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
 
+## Annoying workaround to prevent formula error with special chars in column headers
+colnames(samples) <- make.names(colnames(samples))
+factors <- make.names(factors)
+
+design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
 
 ## DESeq
 

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl

@@ -2,7 +2,7 @@ cwlVersion: v1.2
 class: CommandLineTool
 hints:
   DockerRequirement:
-    dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+    dockerPull: mcr.microsoft.com/dotnet/sdk:8.0
 requirements:
   - class: InitialWorkDirRequirement
     listing:
@@ -25,12 +25,12 @@ inputs:
     type: string
     inputBinding:
       position: 2
-  outName:
-    type: string
-    inputBinding:
-      position: 3
   startingNodeNum:
     type: int
+    inputBinding:
+      position: 3
+  outName:
+    type: string
     inputBinding:
       position: 4
 
@@ -39,5 +39,5 @@ outputs:
     type: File[]
     outputBinding:
       glob:
-        - "*.tsv"
+        - "*.csv"
         - "*.xlsx"

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

@@ -4,22 +4,22 @@
 
 #r "nuget: ARCtrl.NET"
 #r "nuget: ARCtrl.QueryModel"
+#r "nuget: FsSpreadsheet.CsvIO"
 
-open System.IO
 open ARCtrl.NET
 open ARCtrl
 open ARCtrl.QueryModel
 open ARCtrl.Helper
-open FsSpreadsheet
 open FsSpreadsheet.Net
+open FsSpreadsheet.CsvIO
 
 // 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]
+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]
 
 
 type ArcTables with
@@ -31,16 +31,16 @@ type ArcTables with
         )
         |> ArcTables
 
-// test parameters
-let source = __SOURCE_DIRECTORY__
-let arcPath = Path.Combine(source, "../../")
-let assayName = "Talinum_RNASeq_minimal"
-let startingNodeNum = 0
-let outName = "rnaseq-samples"
+// // test parameters
+// let source = __SOURCE_DIRECTORY__
+// let arcPath = Path.Combine(source, "../../")
+// let assayName = "Talinum_RNASeq_minimal"
+// let startingNodeNum = 0
+// let outName = "rnaseq-samples"
 
 // Load ARC
 
-// Remove all tables with either an input or output column missing 🤣😀
+// Remove all tables with either an input or output column missing
 let clean (a : ARC)  = 
     a.ISA.Value.Assays |> Seq.iter (fun a -> 
         a.Tables
@@ -64,7 +64,7 @@ let clean (a : ARC)  =
     )
     a
 
-// transform all data cells to freetext cells 😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀
+// transform all data cells to freetext cells
 let shittify (a : ARC) = 
     a.ISA.Value.Assays |> Seq.iter (fun a -> 
         a.Tables
@@ -161,6 +161,8 @@ let wb = new FsSpreadsheet.FsWorkbook()
 
 wb.AddWorksheet ws
 
-// Write to csv
+// Write to xlsx
+wb.ToXlsxFile ($"{outName}.xlsx")
 
-wb.ToXlsxFile (outName + ".xlsx")
+// Write to csv
\ No newline at end of file
+wb.ToCsvFile ($"{outName}.csv")
\ No newline at end of file