From 6c9a0b879ff7f673a8d2ece1d4aaaa953083a506 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 14 Mar 2025 08:49:19 +0100
Subject: [PATCH] align with spec: deseq2 (needs fix, missing dep)
---
runs/deseq2-run/README.md | 10 --------
runs/deseq2/run.cwl | 24 +++++++++++++++++++
runs/{deseq2-run/job.yml => deseq2/run.yml} | 0
workflows/deseq2/README.md | 5 ----
workflows/deseq2/{deseq2.cwl => workflow.cwl} | 0
5 files changed, 24 insertions(+), 15 deletions(-)
delete mode 100644 runs/deseq2-run/README.md
create mode 100644 runs/deseq2/run.cwl
rename runs/{deseq2-run/job.yml => deseq2/run.yml} (100%)
rename workflows/deseq2/{deseq2.cwl => workflow.cwl} (100%)
diff --git a/runs/deseq2-run/README.md b/runs/deseq2-run/README.md
deleted file mode 100644
index f416fa7..0000000
--- a/runs/deseq2-run/README.md
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-```bash
-cd runs/deseq2-run
-```
-
-```bash
-cwltool ../../workflows/deseq2/deseq2.cwl job.yml
-```
diff --git a/runs/deseq2/run.cwl b/runs/deseq2/run.cwl
new file mode 100644
index 0000000..849cd98
--- /dev/null
+++ b/runs/deseq2/run.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+ inKallistoResults: Directory
+ inMetadataFile: File
+ inMetadataSample: string
+ inMetadataFactorList: string[]
+
+steps:
+ deseq2:
+ run: ../../workflows/deseq2/workflow.cwl
+ in:
+ inKallistoResults: inKallistoResults
+ inMetadataFile: inMetadataFile
+ inMetadataSample: inMetadataSample
+ inMetadataFactorList: inMetadataFactorList
+ out: [output]
+
+outputs:
+ output:
+ type: File[]
+ outputSource: deseq2/output
diff --git a/runs/deseq2-run/job.yml b/runs/deseq2/run.yml
similarity index 100%
rename from runs/deseq2-run/job.yml
rename to runs/deseq2/run.yml
diff --git a/workflows/deseq2/README.md b/workflows/deseq2/README.md
index 39cf2dc..4a64681 100644
--- a/workflows/deseq2/README.md
+++ b/workflows/deseq2/README.md
@@ -35,11 +35,6 @@ RScript deseq2.R "../../runs/kallisto/kallisto_results" "../../runs/merged_isa_m
```
-## Run CWL-wrapped script
-
-see [runs/deseq2-run](../../runs/deseq2-run)
-
-
## Multi-package containers
- R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
diff --git a/workflows/deseq2/deseq2.cwl b/workflows/deseq2/workflow.cwl
similarity index 100%
rename from workflows/deseq2/deseq2.cwl
rename to workflows/deseq2/workflow.cwl
--
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