From 41cb48b58c5701fe55dcb819bee75c6933cc9cd0 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 28 Mar 2025 10:11:16 +0100
Subject: [PATCH] update sub

---
 .cwl/README.md | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++
 .cwl/cwl-aux   |  2 +-
 2 files changed, 93 insertions(+), 1 deletion(-)
 create mode 100644 .cwl/README.md

diff --git a/.cwl/README.md b/.cwl/README.md
new file mode 100644
index 0000000..6b3f620
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+++ b/.cwl/README.md
@@ -0,0 +1,92 @@
+# CWL
+
+<!-- 
+add this repo as submodule to ARCs
+
+```bash
+git submodule add https://git.nfdi4plants.org/brilator/cwl-aux.git .cwl/cwl-aux
+git submodule update --init --recursive
+git submodule update --recursive --remote
+``
+
+ -->
+
+**Data analysis** in this ARC is packaged and made reusable via [Common Workflow Language (CWL)](https://www.commonwl.org).
+For details, visit the [DataPLANT knowledgebase](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/cwl/).
+
+Briefly, every data analysis step (`runs`) is described with a `run.cwl` document. The `run.cwl` points (i.e. executes) one or multiple `workflows` (stored as `workflow.cwl`). The input parameters required for the `workflow.cwl` are documented in the accompanying `run.yml`. A `workflow.cwl` can be a single command line tool or a more complex workflow pipeline that references and combines other `*.cwl` documents.
+
+```bash
+...
+├── runs
+│   ├── fastqc
+│   │   ├── run.cwl
+│   │   └── run.yml
+│   ...
+├── studies
+│   ├── ...
+│
+└── workflows
+    ├── fastqc
+    │   ├── collectFilesInDir.cwl
+    │   ├── fastqc.cwl
+    │   └── workflow.cwl
+    ...
+```
+
+```mermaid
+flowchart TD
+workflowcwl --- runcwl
+subgraph r["runs/fastqc/"]
+    runcwl(("run.cwl"))
+    runyml(("run.yml"))
+end
+i[input: DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz] --- runyml
+r ---> o[output: DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html]
+subgraph "workflows/fastqc"
+    workflowcwl(("workflow.cwl"))
+end
+```
+
+
+## Setup and dependencies
+
+Again, for details check the docs linked above.
+Executing cwl documents requires a cwl runner, e.g. [cwltool](https://github.com/common-workflow-language/cwltool).
+Software and package dependencies are ideally covered by Docker or Conda and described in the hints / requirements sections of cwl documents (e.g. `DockerRequirement` and / or `SoftwareRequirement`).
+
+Additional dependencies may exist for one or the other workflow (e.g. a local installation of R or F# or packages therein), if the workflow is not yet packaged perfectly reusable.
+
+## Default cwltool commands
+
+Here's a list of frequently used `cwltool` commands to validate or execute runs and workflows.
+
+### Validate document
+
+```bash
+cwltool --validate run.cwl
+```
+
+### Execute workflow in `./runs/*`
+
+```bash
+cwltool run.cwl run.yml
+```
+
+### capture log and run in bg
+
+```bash
+cwltool run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
+```
+
+### capture log, run in parallel and in bg
+
+```bash
+cwltool --parallel --timestamp run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
+```
+
+### Print workflow to file
+
+```bash
+cwltool --print-dot ../arc.cwl | dot -Tsvg > arc-cwl.svg
+```
diff --git a/.cwl/cwl-aux b/.cwl/cwl-aux
index 11931ea..a2d591e 160000
--- a/.cwl/cwl-aux
+++ b/.cwl/cwl-aux
@@ -1 +1 @@
-Subproject commit 11931eaf85d05574e9a8c0aff32de00a6f3a46d7
+Subproject commit a2d591e879b619161d6482d5552a9d287691b99a
-- 
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