From a3a1fdb80180bf080235d05c95a1c0f330c5d8b2 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 7 Nov 2024 16:04:39 +0100
Subject: [PATCH] fix isa sample process reader
---
runs/isaSampleToRawDataSeq-run/README.md | 2 +-
runs/isaSampleToRawDataSeq-run/job.yml | 2 +-
.../rnaseq-samples.csv | 7 ++++
.../rnaseq-samples.xlsx | Bin 0 -> 7112 bytes
.../isaSampleToRawDataSeq.cwl | 12 +++---
.../isaSampleToRawDataSeq.fsx | 36 +++++++++---------
6 files changed, 34 insertions(+), 25 deletions(-)
create mode 100644 runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv
create mode 100644 runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx
diff --git a/runs/isaSampleToRawDataSeq-run/README.md b/runs/isaSampleToRawDataSeq-run/README.md
index d8e1dcb..6c83a17 100644
--- a/runs/isaSampleToRawDataSeq-run/README.md
+++ b/runs/isaSampleToRawDataSeq-run/README.md
@@ -2,7 +2,7 @@
```bash
-cd runs/isaSampleToRawDataSeq
+cd runs/isaSampleToRawDataSeq-run
```
```bash
diff --git a/runs/isaSampleToRawDataSeq-run/job.yml b/runs/isaSampleToRawDataSeq-run/job.yml
index 803a637..2c640ff 100644
--- a/runs/isaSampleToRawDataSeq-run/job.yml
+++ b/runs/isaSampleToRawDataSeq-run/job.yml
@@ -2,5 +2,5 @@ arcPath:
class: Directory
path: ../../
assayName: "Talinum_RNASeq_minimal"
-outName: "rnaseq-samples"
+outName: rnaseq-samples
startingNodeNum: 1
diff --git a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv b/runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv
new file mode 100644
index 0000000..ca63a9d
--- /dev/null
+++ b/runs/isaSampleToRawDataSeq-run/rnaseq-samples.csv
@@ -0,0 +1,7 @@
+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_ext,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_ext,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_ext,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_ext,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_ext,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_ext,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
diff --git a/runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx b/runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx
new file mode 100644
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diff --git a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl b/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl
index a00b3e8..e743f32 100644
--- a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl
+++ b/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"
diff --git a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx b/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
index 20ba577..5ac29ad 100644
--- a/workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx
+++ b/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 ($"{outName}.xlsx")
-wb.ToXlsxFile (outName + ".xlsx")
\ No newline at end of file
+// Write to csv
+wb.ToCsvFile ($"{outName}.csv")
\ No newline at end of file
--
GitLab