From 00fa74c216e589dae0998b6beb58a356f0991da0 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Wed, 19 Mar 2025 15:00:20 +0100
Subject: [PATCH] improve logic to gather output directories from kallisto
scatter step
---
.cwl/cwl-plots/runs/kallisto.svg | 10 +++++-----
.cwl/cwl-plots/workflows/kallisto.svg | 10 +++++-----
arc.cwl | 4 ++--
.../isaSampleToRawDataSeq/rnaseq-samples.xlsx | Bin 7183 -> 7184 bytes
runs/isaSampleToRawDataSeq/run.cwl | 13 ++++++++++---
runs/kallisto/run.cwl | 8 ++++----
workflows/isaSampleToRawDataSeq/workflow.cwl | 8 ++++++--
...d-dirInDestination.cwl => gather-dirs.cwl} | 6 +++---
workflows/kallisto/kallisto-quant.cwl | 2 +-
workflows/kallisto/workflow.cwl | 13 ++++++-------
10 files changed, 42 insertions(+), 32 deletions(-)
rename workflows/kallisto/{yield-dirInDestination.cwl => gather-dirs.cwl} (64%)
diff --git a/.cwl/cwl-plots/runs/kallisto.svg b/.cwl/cwl-plots/runs/kallisto.svg
index 45f69bc..241535b 100644
--- a/.cwl/cwl-plots/runs/kallisto.svg
+++ b/.cwl/cwl-plots/runs/kallisto.svg
@@ -109,15 +109,15 @@
<path fill="none" stroke="black" d="M79.18,-185.43C89.76,-174.74 104.84,-161.76 121,-155 157.69,-139.66 267.22,-133.56 330.49,-131.27"/>
<polygon fill="black" stroke="black" points="330.73,-134.77 340.61,-130.93 330.49,-127.77 330.73,-134.77"/>
</g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
<g id="node9" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
<polygon fill="#94ddf4" stroke="black" points="346.06,-38.5 346.06,-74.5 407.94,-74.5 407.94,-38.5 346.06,-38.5"/>
-<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="377" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
</g>
-<!-- kallisto->finalOut -->
+<!-- kallisto->kallistoOutDir -->
<g id="edge8" class="edge">
-<title>kallisto->finalOut</title>
+<title>kallisto->kallistoOutDir</title>
<path fill="none" stroke="black" d="M377,-110.93C377,-103.17 377,-93.78 377,-85.06"/>
<polygon fill="black" stroke="black" points="380.5,-84.9 377,-74.9 373.5,-84.9 380.5,-84.9"/>
</g>
diff --git a/.cwl/cwl-plots/workflows/kallisto.svg b/.cwl/cwl-plots/workflows/kallisto.svg
index 9e81b88..930b4ca 100644
--- a/.cwl/cwl-plots/workflows/kallisto.svg
+++ b/.cwl/cwl-plots/workflows/kallisto.svg
@@ -37,15 +37,15 @@
<path fill="none" stroke="black" d="M491.95,-193.08C456.78,-182.13 394.44,-162.71 348.49,-148.4"/>
<polygon fill="black" stroke="black" points="349.25,-144.97 338.66,-145.34 347.16,-151.66 349.25,-144.97"/>
</g>
-<!-- finalOut -->
+<!-- kallistoOutDir -->
<g id="node11" class="node">
-<title>finalOut</title>
+<title>kallistoOutDir</title>
<polygon fill="#94ddf4" stroke="black" points="260.06,-38.5 260.06,-74.5 321.94,-74.5 321.94,-38.5 260.06,-38.5"/>
-<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">finalOut</text>
+<text text-anchor="middle" x="291" y="-52.3" font-family="Times,serif" font-size="14.00">kallistoOutDir</text>
</g>
-<!-- collectResults->finalOut -->
+<!-- collectResults->kallistoOutDir -->
<g id="edge12" class="edge">
-<title>collectResults->finalOut</title>
+<title>collectResults->kallistoOutDir</title>
<path fill="none" stroke="black" d="M291,-111.31C291,-103.29 291,-93.55 291,-84.57"/>
<polygon fill="black" stroke="black" points="294.5,-84.53 291,-74.53 287.5,-84.53 294.5,-84.53"/>
</g>
diff --git a/arc.cwl b/arc.cwl
index 0043dcf..e42113e 100644
--- a/arc.cwl
+++ b/arc.cwl
@@ -50,7 +50,7 @@ steps:
StandardDeviation: kallisto_StandardDeviation
BootstrapSamples: kallisto_BootstrapSamples
resultsFolder: kallisto_resultsFolder
- out: [finalOut]
+ out: [kallistoOutDir]
isaSampleToRawDataSeq:
@@ -65,7 +65,7 @@ steps:
sleuth:
run: runs/sleuth/run.cwl
in:
- inKallistoResults: kallisto/finalOut
+ inKallistoResults: kallisto/kallistoOutDir
inMetadataFile: isaSampleToRawDataSeq/output
inMetadataSample: sleuth_inMetadataSample
inMetadataFactorList: sleuth_inMetadataFactorList
diff --git a/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx b/runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx
index 1c05d363efc105474dc4887ac57f94beba0ac181..e73d722501815a8b129f9f7a95b3b0af60c45ab0 100644
GIT binary patch
delta 748
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delta 769
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diff --git a/runs/isaSampleToRawDataSeq/run.cwl b/runs/isaSampleToRawDataSeq/run.cwl
index 8f00f6a..3df9da4 100644
--- a/runs/isaSampleToRawDataSeq/run.cwl
+++ b/runs/isaSampleToRawDataSeq/run.cwl
@@ -1,6 +1,9 @@
cwlVersion: v1.2
class: Workflow
+requirements:
+ MultipleInputFeatureRequirement: {}
+
inputs:
arcPath: Directory
assayName: string
@@ -15,10 +18,14 @@ steps:
assayName: assayName
startingNodeNum: startingNodeNum
outName: outName
- out: [output]
+ out:
+ - sampleseqCsv
+ - sampleseqXlsx
outputs:
- output:
+ sampleseqs:
type: File[]
- outputSource: isaSampleToRawDataSeq/output
+ outputSource:
+ - isaSampleToRawDataSeq/sampleseqCsv
+ - isaSampleToRawDataSeq/sampleseqXlsx
diff --git a/runs/kallisto/run.cwl b/runs/kallisto/run.cwl
index 3ec2a22..d702ed4 100644
--- a/runs/kallisto/run.cwl
+++ b/runs/kallisto/run.cwl
@@ -35,9 +35,9 @@ steps:
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
resultsFolder: resultsFolder
- out: [finalOut]
+ out: [kallistoOutDir]
outputs:
- finalOut:
- type: Directory[]
- outputSource: kallisto/finalOut
+ kallistoOutDir:
+ type: Directory
+ outputSource: kallisto/kallistoOutDir
diff --git a/workflows/isaSampleToRawDataSeq/workflow.cwl b/workflows/isaSampleToRawDataSeq/workflow.cwl
index 9cace45..f9db3ee 100644
--- a/workflows/isaSampleToRawDataSeq/workflow.cwl
+++ b/workflows/isaSampleToRawDataSeq/workflow.cwl
@@ -39,9 +39,13 @@ inputs:
position: 4
outputs:
- output:
- type: File[]
+ sampleseqCsv:
+ type: File
outputBinding:
glob:
- "*.csv"
+ sampleseqXlsx:
+ type: File
+ outputBinding:
+ glob:
- "*.xlsx"
diff --git a/workflows/kallisto/yield-dirInDestination.cwl b/workflows/kallisto/gather-dirs.cwl
similarity index 64%
rename from workflows/kallisto/yield-dirInDestination.cwl
rename to workflows/kallisto/gather-dirs.cwl
index bc90cb8..c7a13f5 100644
--- a/workflows/kallisto/yield-dirInDestination.cwl
+++ b/workflows/kallisto/gather-dirs.cwl
@@ -1,18 +1,18 @@
cwlVersion: v1.2
class: ExpressionTool
doc: |
- Takes a directory (e.g. from a workflow step) and yields it in a desired directory.
+ Takes an array of directories (e.g. from a workflow step) and yields them in a destination directory.
requirements:
- class: InlineJavascriptRequirement
inputs:
- inDir: Directory
+ inDirs: Directory[]
destinationDir: string
expression: |
${
return {"outDir": {
"class": "Directory",
"basename": inputs.destinationDir,
- "listing": [inputs.inDir]
+ "listing": inputs.inDirs
} };
}
outputs:
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 026f7e1..692be58 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -126,7 +126,7 @@ arguments: [ "--output-dir", $(inputs.QuantOutfolder) ]
outputs:
- outFolder:
+ kallistoQuantOutDir:
type: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.QuantOutfolder)
diff --git a/workflows/kallisto/workflow.cwl b/workflows/kallisto/workflow.cwl
index 4ce5617..56e1400 100644
--- a/workflows/kallisto/workflow.cwl
+++ b/workflows/kallisto/workflow.cwl
@@ -51,17 +51,16 @@ steps:
FragmentLength: FragmentLength
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
- out: [outFolder]
-
+ out: [kallistoQuantOutDir]
collectResults:
- run: ./yield-dirInDestination.cwl
- scatter: inDir
+ run: ./gather-dirs.cwl
in:
- inDir: quant/outFolder
+ inDirs: quant/kallistoQuantOutDir
destinationDir: resultsFolder
out: [outDir]
outputs:
- finalOut:
- type: Directory[]
+ kallistoOutDir:
+ type: Directory
outputSource: collectResults/outDir
+
--
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