From e4f723243e174e59b8a512cfb7a383cf142cc1a6 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 28 Mar 2025 10:14:37 +0100
Subject: [PATCH] add cwl plots to READMEs

---
 runs/deseq2/README.md                | 9 +++++++++
 runs/fastqc/README.md                | 9 +++++++++
 runs/isaSampleToRawDataSeq/README.md | 9 +++++++++
 runs/kallisto/README.md              | 9 +++++++++
 runs/shiny/README.md                 | 9 +++++++++
 runs/sleuth/README.md                | 9 +++++++++
 workflows/deseq2/README.md           | 9 +++++++++
 workflows/fastqc/README.md           | 9 +++++++++
 workflows/kallisto/README.md         | 9 +++++++++
 workflows/sleuth/README.md           | 9 +++++++++
 10 files changed, 90 insertions(+)
 create mode 100644 runs/deseq2/README.md
 create mode 100644 runs/fastqc/README.md
 create mode 100644 runs/isaSampleToRawDataSeq/README.md
 create mode 100644 runs/kallisto/README.md
 create mode 100644 runs/shiny/README.md
 create mode 100644 runs/sleuth/README.md
 create mode 100644 workflows/deseq2/README.md
 create mode 100644 workflows/fastqc/README.md
 create mode 100644 workflows/kallisto/README.md
 create mode 100644 workflows/sleuth/README.md

diff --git a/runs/deseq2/README.md b/runs/deseq2/README.md
new file mode 100644
index 0000000..78e8f8e
--- /dev/null
+++ b/runs/deseq2/README.md
@@ -0,0 +1,9 @@
+# deseq2
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/runs/fastqc/README.md b/runs/fastqc/README.md
new file mode 100644
index 0000000..6dc50e4
--- /dev/null
+++ b/runs/fastqc/README.md
@@ -0,0 +1,9 @@
+# fastqc
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/runs/isaSampleToRawDataSeq/README.md b/runs/isaSampleToRawDataSeq/README.md
new file mode 100644
index 0000000..a81f6c2
--- /dev/null
+++ b/runs/isaSampleToRawDataSeq/README.md
@@ -0,0 +1,9 @@
+# isaSampleToRawDataSeq
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/runs/kallisto/README.md b/runs/kallisto/README.md
new file mode 100644
index 0000000..498e501
--- /dev/null
+++ b/runs/kallisto/README.md
@@ -0,0 +1,9 @@
+# kallisto
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/runs/shiny/README.md b/runs/shiny/README.md
new file mode 100644
index 0000000..406c32f
--- /dev/null
+++ b/runs/shiny/README.md
@@ -0,0 +1,9 @@
+# shiny
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/runs/sleuth/README.md b/runs/sleuth/README.md
new file mode 100644
index 0000000..f0b57d2
--- /dev/null
+++ b/runs/sleuth/README.md
@@ -0,0 +1,9 @@
+# sleuth
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](run.svg)
+
+<!-- cwlplot -->
diff --git a/workflows/deseq2/README.md b/workflows/deseq2/README.md
new file mode 100644
index 0000000..e2092df
--- /dev/null
+++ b/workflows/deseq2/README.md
@@ -0,0 +1,9 @@
+# deseq2
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](workflow.svg)
+
+<!-- cwlplot -->
diff --git a/workflows/fastqc/README.md b/workflows/fastqc/README.md
new file mode 100644
index 0000000..5112bd6
--- /dev/null
+++ b/workflows/fastqc/README.md
@@ -0,0 +1,9 @@
+# fastqc
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](workflow.svg)
+
+<!-- cwlplot -->
diff --git a/workflows/kallisto/README.md b/workflows/kallisto/README.md
new file mode 100644
index 0000000..fd6515c
--- /dev/null
+++ b/workflows/kallisto/README.md
@@ -0,0 +1,9 @@
+# kallisto
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](workflow.svg)
+
+<!-- cwlplot -->
diff --git a/workflows/sleuth/README.md b/workflows/sleuth/README.md
new file mode 100644
index 0000000..f0d4b67
--- /dev/null
+++ b/workflows/sleuth/README.md
@@ -0,0 +1,9 @@
+# sleuth
+
+<!-- cwlplot -->
+
+## Workflow overview
+
+![](workflow.svg)
+
+<!-- cwlplot -->
-- 
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