From 211ac2be5acdf160d1e7394d773c5b2875636773 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Mon, 24 Mar 2025 10:17:13 +0100
Subject: [PATCH] redesign sleuth
---
runs/sleuth/run.cwl | 14 ++--
runs/sleuth/run.yml | 2 +-
workflows/sleuth/gather-files.cwl | 24 +++++++
workflows/sleuth/sleuth.R | 23 ++----
workflows/sleuth/sleuth.cwl | 87 +++++++++++++++++++++++
workflows/sleuth/workflow.cwl | 113 +++++++++++++++---------------
6 files changed, 182 insertions(+), 81 deletions(-)
create mode 100644 workflows/sleuth/gather-files.cwl
create mode 100644 workflows/sleuth/sleuth.cwl
diff --git a/runs/sleuth/run.cwl b/runs/sleuth/run.cwl
index 7884d8d..789736f 100644
--- a/runs/sleuth/run.cwl
+++ b/runs/sleuth/run.cwl
@@ -3,13 +3,16 @@
cwlVersion: v1.2
class: Workflow
+requirements:
+ SubworkflowFeatureRequirement: {}
+
inputs:
inKallistoResults: Directory
inMetadataFile: File
inMetadataSample: string
inMetadataFactorList: string[]
inMetadataDataCol: string
- outFolder: string
+ resultsoutdir: string
steps:
sleuth:
@@ -20,14 +23,13 @@ steps:
inMetadataSample: inMetadataSample
inMetadataFactorList: inMetadataFactorList
inMetadataDataCol: inMetadataDataCol
- outFolder: outFolder
- out: [outdir]
+ finaloutdir: resultsoutdir
+ out: [ sleuth_outdir ]
outputs:
outdir:
- type: Directory[]
- outputSource: sleuth/outdir
-
+ type: Directory
+ outputSource: sleuth/sleuth_outdir
$namespaces:
s: https://schema.org/
diff --git a/runs/sleuth/run.yml b/runs/sleuth/run.yml
index 1996f50..61c509d 100644
--- a/runs/sleuth/run.yml
+++ b/runs/sleuth/run.yml
@@ -8,4 +8,4 @@ inMetadataSample: "Input [Source Name]"
inMetadataFactorList:
- "Factor [Photosynthesis mode]"
inMetadataDataCol: "Output [Data]"
-outFolder: results
+resultsoutdir: results
diff --git a/workflows/sleuth/gather-files.cwl b/workflows/sleuth/gather-files.cwl
new file mode 100644
index 0000000..67d23ec
--- /dev/null
+++ b/workflows/sleuth/gather-files.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.2
+class: ExpressionTool
+label: Gather files
+doc: |
+ Helper tool to organize workflow outputs
+
+ Takes an array of files (e.g. from a workflow step) and yields them in a destination directory.
+
+ Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
+requirements:
+ - class: InlineJavascriptRequirement
+inputs:
+ inFiles: File[]
+ destination: string
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destination,
+ "listing": inputs.inFiles
+ } };
+ }
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/sleuth/sleuth.R b/workflows/sleuth/sleuth.R
index 2b2283c..a9e0b52 100644
--- a/workflows/sleuth/sleuth.R
+++ b/workflows/sleuth/sleuth.R
@@ -18,7 +18,6 @@ inMetadataFile <- args[2]
inMetadataSample <- args[3]
inMetadataFactorList <- args[4]
inMetadataDataCol <- args[5]
-outFolder <- args[6]
# inKallistoResults <- "../../runs/kallisto/kallisto_results"
# inMetadataFile <- "../../runs/isaSampleToRawDataSeq/rnaseq-samples.csv"
@@ -27,12 +26,6 @@ outFolder <- args[6]
# inMetadataDataCol <- "Output [Data]"
# outFolder <- "."
-################################################
-#### If it does not exist, create out dir
-################################################
-
-dir.create(outFolder, recursive = T, showWarnings = F)
-
################################################
#### Read ISA sample metadata
################################################
@@ -43,10 +36,8 @@ samples <- read.csv(file = inMetadataFile, check.names = FALSE)
#### Read Kallisto results
################################################
-base_dir <- inKallistoResults
-
# A list of paths to the kallisto results indexed by the sample IDs is collated with
-kal_dirs <- dir(base_dir, full.names = T) ## Sleuth requires full paths
+kal_dirs <- dir(inKallistoResults, full.names = T) ## Sleuth requires full paths
s2c <- samples[order(samples[[inMetadataSample]]), c(inMetadataSample, unlist(inMetadataFactorList), inMetadataDataCol)]
@@ -66,7 +57,7 @@ design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
so <- sleuth_prep(s2c, full_model = design_formula)
-save(so, file = file.path(outFolder, "kallisto_sleuthObject.RData"))
+save(so, file = "kallisto_sleuthObject.RData")
################################################
#### Extract expression tables
@@ -76,13 +67,13 @@ save(so, file = file.path(outFolder, "kallisto_sleuthObject.RData"))
expression_data <- kallisto_table(so)
## write to file
-write.csv(expression_data, file.path(outFolder, "kallisto_df.csv"), row.names = F)
+write.csv(expression_data, "kallisto_df.csv", row.names = F)
## as tpm matrix (gene x sample)
tpm_table <- reshape(expression_data, idvar = "target_id", timevar = "sample", direction = "wide", v.names = "tpm")
# Write to file
-write.csv(tpm_table, file.path(outFolder, "kallisto_tpmMatrix.csv"), row.names = F)
+write.csv(tpm_table, "kallisto_tpmMatrix.csv", row.names = F)
################################################
#### Summarize mapping stats
@@ -95,11 +86,11 @@ for (i in dir(kal_dirs, pattern = ".json", full.names = T)) {
mapping_stats <- rbind(mapping_stats, z)
}
-write.csv(mapping_stats, file.path(outFolder, "kallisto_mappingStats.csv"), row.names = F)
+write.csv(mapping_stats, "kallisto_mappingStats.csv", row.names = F)
################################################
-#### Run sleuth to identify DEGs
+#### Run sleuth to identify DGE
################################################
so <- sleuth_fit(so)
@@ -111,4 +102,4 @@ sleuth_table <- sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
### write to file
-write.csv(sleuth_table, file.path(outFolder, "sleuth_dge.csv"), row.names = F)
+write.csv(sleuth_table, "sleuth_dge.csv", row.names = F)
diff --git a/workflows/sleuth/sleuth.cwl b/workflows/sleuth/sleuth.cwl
new file mode 100644
index 0000000..3ffc997
--- /dev/null
+++ b/workflows/sleuth/sleuth.cwl
@@ -0,0 +1,87 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0
+ SoftwareRequirement:
+ packages:
+ - package: R
+ specs:
+ - https://identifiers.org/rrid/RRID:SCR_001905
+ - https://identifiers.org/biotools/r
+ - https://anaconda.org/bioconda/r
+ version: [ "4.2.3" ]
+ - package: sleuth
+ version: [ "0.30.1" ]
+ specs:
+ - https://identifiers.org/rrid/RRID:SCR_016883
+ - https://identifiers.org/biotools/sleuth
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: sleuth.R
+ entry:
+ $include: sleuth.R
+
+baseCommand: [Rscript, sleuth.R]
+
+inputs:
+ inKallistoResults:
+ type: Directory
+ inputBinding:
+ position: 1
+ inMetadataFile:
+ type: File
+ inputBinding:
+ position: 2
+ inMetadataSample:
+ type: string
+ inputBinding:
+ position: 3
+ inMetadataFactorList:
+ type: string[]
+ inputBinding:
+ position: 4
+ inMetadataDataCol:
+ type: string
+ inputBinding:
+ position: 5
+
+outputs:
+ kallisto_sleuthObject:
+ type: File
+ outputBinding:
+ glob: "kallisto_sleuthObject.RData"
+ kallisto_df:
+ type: File
+ outputBinding:
+ glob: "kallisto_df.csv"
+ kallisto_tpmMatrix:
+ type: File
+ outputBinding:
+ glob: "kallisto_tpmMatrix.csv"
+ kallisto_mappingStats:
+ type: File
+ outputBinding:
+ glob: "kallisto_mappingStats.csv"
+ sleuth_dge:
+ type: File
+ outputBinding:
+ glob: "sleuth_dge.csv"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
\ No newline at end of file
diff --git a/workflows/sleuth/workflow.cwl b/workflows/sleuth/workflow.cwl
index 497533c..5f08a47 100644
--- a/workflows/sleuth/workflow.cwl
+++ b/workflows/sleuth/workflow.cwl
@@ -1,66 +1,63 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2
-class: CommandLineTool
-
-hints:
- DockerRequirement:
- dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0
- SoftwareRequirement:
- packages:
- - package: R
- specs:
- - https://identifiers.org/rrid/RRID:SCR_001905
- - https://identifiers.org/biotools/r
- - https://anaconda.org/bioconda/r
- version: [ "4.2.3" ]
- - package: sleuth
- version: [ "0.30.1" ]
- specs:
- - https://identifiers.org/rrid/RRID:SCR_016883
- - https://identifiers.org/biotools/sleuth
+class: Workflow
requirements:
- - class: InitialWorkDirRequirement
- listing:
- - entryname: sleuth.R
- entry:
- $include: sleuth.R
- # - class: NetworkAccess
- # networkAccess: true
-
-baseCommand: [Rscript, sleuth.R]
+ ScatterFeatureRequirement: {}
+ SubworkflowFeatureRequirement: {}
+ MultipleInputFeatureRequirement: {}
inputs:
- inKallistoResults:
+ inKallistoResults: Directory
+ inMetadataFile: File
+ inMetadataSample: string
+ inMetadataFactorList: string[]
+ inMetadataDataCol: string
+ finaloutdir: string
+
+steps:
+ sleuth:
+ run: sleuth.cwl
+ in:
+ inKallistoResults: inKallistoResults
+ inMetadataFile: inMetadataFile
+ inMetadataSample: inMetadataSample
+ inMetadataFactorList: inMetadataFactorList
+ inMetadataDataCol: inMetadataDataCol
+ out:
+ - kallisto_sleuthObject
+ - kallisto_df
+ - kallisto_tpmMatrix
+ - kallisto_mappingStats
+ - sleuth_dge
+ collectFiles:
+ run: ./gather-files.cwl
+ in:
+ inFiles:
+ source:
+ - sleuth/kallisto_sleuthObject
+ - sleuth/kallisto_df
+ - sleuth/kallisto_tpmMatrix
+ - sleuth/kallisto_mappingStats
+ - sleuth/sleuth_dge
+ linkMerge: merge_flattened
+ destination: finaloutdir
+ out: [outDir]
+
+outputs:
+ sleuth_outdir:
type: Directory
- inputBinding:
- position: 1
- inMetadataFile:
- type: File
- inputBinding:
- position: 2
- inMetadataSample:
- type: string
- inputBinding:
- position: 3
- inMetadataFactorList:
- type: string[]
- inputBinding:
- position: 4
- inMetadataDataCol:
- type: string
- inputBinding:
- position: 5
- outFolder:
- type: string
- inputBinding:
- position: 6
+ outputSource: collectFiles/outDir
-outputs:
-- id: outdir
- type:
- type: array
- items: Directory
- outputBinding:
- glob: $(runtime.outdir)/$(inputs.outFolder)
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schemaorg-current-https.rdf
+ - http://edamontology.org/EDAM_1.18.owl
+
+s:author:
+ - class: s:Person
+ s:name: Dominik Brilhaus
+ s:identifier: https://orcid.org/0000-0001-9021-3197
--
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