From 7efff5719fb31283668259210a89b5223358a25e Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 14 Mar 2025 09:47:31 +0100
Subject: [PATCH] remove cwl aux-tools
---
runs/.gitkeep | 0
workflows/_aux-tools/collectFilesInDir.cwl | 19 -------------------
workflows/kallisto/kallisto-workflow.cwl | 2 +-
.../yield-dirInDestination.cwl | 0
workflows/merge_isa_metadata/placeholder.cwl | 1 -
5 files changed, 1 insertion(+), 21 deletions(-)
delete mode 100644 runs/.gitkeep
delete mode 100644 workflows/_aux-tools/collectFilesInDir.cwl
rename workflows/{_aux-tools => kallisto}/yield-dirInDestination.cwl (100%)
delete mode 100644 workflows/merge_isa_metadata/placeholder.cwl
diff --git a/runs/.gitkeep b/runs/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/workflows/_aux-tools/collectFilesInDir.cwl b/workflows/_aux-tools/collectFilesInDir.cwl
deleted file mode 100644
index f8d411f..0000000
--- a/workflows/_aux-tools/collectFilesInDir.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-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/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index e7f0350..1d020e1 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -57,7 +57,7 @@ steps:
BootstrapSamples: BootstrapSamples
out: [outFolder]
collectResults:
- run: ../_aux-tools/yield-dirInDestination.cwl
+ run: ./yield-dirInDestination.cwl
scatter: inDir
in:
inDir: quant/outFolder
diff --git a/workflows/_aux-tools/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl
similarity index 100%
rename from workflows/_aux-tools/yield-dirInDestination.cwl
rename to workflows/kallisto/yield-dirInDestination.cwl
diff --git a/workflows/merge_isa_metadata/placeholder.cwl b/workflows/merge_isa_metadata/placeholder.cwl
deleted file mode 100644
index 30d74d2..0000000
--- a/workflows/merge_isa_metadata/placeholder.cwl
+++ /dev/null
@@ -1 +0,0 @@
-test
\ No newline at end of file
--
GitLab