From 312c490768d2d2fd653741f130ca02c54bf9fbb1 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 2 Aug 2024 14:52:19 +0200
Subject: [PATCH] collect results in single folder
---
runs/kallisto/workflow.yml | 11 +++++++----
workflows/_aux-tools/collectFilesInDir.cwl | 19 +++++++++++++++++++
.../_aux-tools/yield-dirInDestination.cwl | 19 +++++++++++++++++++
workflows/kallisto/kallisto-workflow.cwl | 15 +++++++++++----
4 files changed, 56 insertions(+), 8 deletions(-)
create mode 100644 workflows/_aux-tools/collectFilesInDir.cwl
create mode 100644 workflows/_aux-tools/yield-dirInDestination.cwl
diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index db33ad6..44b12a5 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -13,17 +13,20 @@ InputReadsMultipleSamples:
- class: File
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
- -
- - class: File
- path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
- format: edam:format_1930 # FASTQ
+ # -
+ # - class: File
+ # path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+ # format: edam:format_1930 # FASTQ
numCharsFastqFileName: 6
+
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
StandardDeviation: 20
BootstrapSamples: 1
+resultsFolder: kallist_results
+
$namespaces:
edam: https://edamontology.org/
\ No newline at end of file
diff --git a/workflows/_aux-tools/collectFilesInDir.cwl b/workflows/_aux-tools/collectFilesInDir.cwl
new file mode 100644
index 0000000..f8d411f
--- /dev/null
+++ b/workflows/_aux-tools/collectFilesInDir.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.2
+class: ExpressionTool
+doc: |
+ Takes Files (e.g. from a workflow step) and yields them in a desired directory.
+requirements:
+ - class: InlineJavascriptRequirement
+inputs:
+ files: File[]
+ destination: string
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destination,
+ "listing": inputs.files
+ } };
+ }
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/_aux-tools/yield-dirInDestination.cwl b/workflows/_aux-tools/yield-dirInDestination.cwl
new file mode 100644
index 0000000..c2a20ea
--- /dev/null
+++ b/workflows/_aux-tools/yield-dirInDestination.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.2
+class: ExpressionTool
+doc: |
+ Takes a directory (e.g. from a workflow step) and yield it in a desired directory.
+requirements:
+ - class: InlineJavascriptRequirement
+inputs:
+ inDir: Directory
+ destinationDir: string
+expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destinationDir,
+ "listing": [inputs.inDir]
+ } };
+ }
+outputs:
+ outDir: Directory
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 0cf46eb..6bbeb9d 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -14,11 +14,11 @@ inputs:
items:
type: array
items: File
- numCharsFastqFileName: int?
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
- BootstrapSamples: int?
+ BootstrapSamples: int?
+ resultsFolder: string
steps:
index:
@@ -46,8 +46,15 @@ steps:
StandardDeviation: StandardDeviation
BootstrapSamples: BootstrapSamples
out: [outFolder]
+ collectResults:
+ run: ../_aux-tools/yield-dirInDestination.cwl
+ scatter: inDir
+ in:
+ inDir: quant/outFolder
+ destinationDir: resultsFolder
+ out: outDir
outputs:
finalOut:
- type: Directory[]
- outputSource: quant/outFolder
+ type: Directory
+ outputSource: collectResults/outDir
--
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