diff --git a/.cwl/README.md b/.cwl/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..c871e53701554c85298f7653a15b25b19062282b
--- /dev/null
+++ b/.cwl/README.md
@@ -0,0 +1,86 @@
+# CWL
+
+**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
+%%{ init: {"flowchart": { "wrappingWidth": "10000" }}}%%
+
+flowchart TD
+
+workflowcwl --o runcwl
+
+subgraph r["runs/fastqc/"]
+ runcwl@{ shape: doc, label: "run.cwl" }
+ runyml@{ shape: doc, label: "run.yml" }
+end
+
+i[input: DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz] --o runyml
+r --> o[output: DB_097_CAMMD_CAGATC_L001_R1_001_fastqc.html]
+
+subgraph "workflows/fastqc"
+ workflowcwl@{ shape: doc, label: "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 run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
+```
+
+### Print workflow to file
+
+```bash
+cwltool --print-dot run.cwl | dot -Tsvg > run.svg
+```
diff --git a/.cwl/cwl-notes.md b/.cwl/cwl-notes.md
deleted file mode 100644
index 61c90a92bb4d21b565c4281b2585ec6474428104..0000000000000000000000000000000000000000
--- a/.cwl/cwl-notes.md
+++ /dev/null
@@ -1,47 +0,0 @@
-# CWL
-
-## Organisation
-
-### Runs
-
-Every run is described with a `run.cwl` workflow that points to (i.e. steps through) one or multiple workflows or tools.
-
-## Default cwltool commands
-
-### 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 run.cwl run.yml > $(date +"%Y-%m-%d_%H-%M")-run.log 2>&1 &
-```
-
-### Print workflow to file
-
-```bash
-cwltool --print-dot run.cwl | dot -Tsvg > run.svg
-```
-
-### List all workflows
-
-```bash
-find ./workflows -name 'workflow.cwl' -exec zsh -c 'echo "$1" >> workflows.txt' zsh {} \;
-find ./workflows -name 'workflow.cwl' -exec zsh -c 'cwltool --validate "$1" > validate-workflows.txt' zsh {} \;
-find ./runs -name 'run.cwl' -exec zsh -c 'cwltool --validate "$1" > validate-runs.txt' zsh {} \;
-```
\ No newline at end of file
diff --git a/.cwl/cwl-plots/README.md b/.cwl/cwl-plots/README.md
deleted file mode 100644
index 5775769923097db75e5c22be238b0a40e5a5ba50..0000000000000000000000000000000000000000
--- a/.cwl/cwl-plots/README.md
+++ /dev/null
@@ -1,4 +0,0 @@
-
-```bash
-bash plot-cwls.sh "../../" "run.cwl" "runs-wfls.txt" "runs"
-```
\ No newline at end of file
diff --git a/.cwl/cwl-plots/plot-cwls.sh b/.cwl/cwl-plots/plot-cwls.sh
index dfa5660bf32ac5dbfa0adce3e995ecc5c876021d..f78df0cc1e64a97416d8a1f9b2695374df91cdb7 100644
--- a/.cwl/cwl-plots/plot-cwls.sh
+++ b/.cwl/cwl-plots/plot-cwls.sh
@@ -1,3 +1,7 @@
+
+
+# Test : `bash plot-cwls.sh "../../" "run.cwl" "runs-wfls.txt" "runs"`
+
arcRoot=$1
cwlPattern=$2
outWflList=$3
@@ -8,8 +12,6 @@ find "$arcRoot"/ -name "$cwlPattern" > "$outWflList"
mkdir -p "$outGraphs"
while IFS= read -r wfl; do
- dirname "$wfl" | xargs basename | xargs read wflname
+ read wflname < <(dirname "$wfl" | xargs basename)
cwltool --print-dot "$wfl" | dot -Tsvg > "$outGraphs"/"$wflname".svg
-done < "$outWflList"
-
-
+done < "$outWflList"
\ No newline at end of file
diff --git a/.cwl/cwl-plots/validate-workflows.yml b/.cwl/cwl-plots/plot-workflows.yml
similarity index 72%
rename from .cwl/cwl-plots/validate-workflows.yml
rename to .cwl/cwl-plots/plot-workflows.yml
index ad62de6fdf30b07d0bd356f268fba0128bd9a315..f2eaecbb545f5bcf08a8cf91cb0de302f3174e04 100644
--- a/.cwl/cwl-plots/validate-workflows.yml
+++ b/.cwl/cwl-plots/plot-workflows.yml
@@ -3,4 +3,4 @@ arcRoot:
path: "../../"
cwlPattern: "workflow.cwl"
outWflList: "workflow-wfls.txt"
-outValidation: "validate-workflows.txt"
\ No newline at end of file
+outGraphs: "workflows"
\ No newline at end of file
diff --git a/.cwl/cwl-plots/plot.cwl b/.cwl/cwl-plots/plot.cwl
index 0cab62619491814ba3e3aec560b11b7a7c081ae6..799d219932612a584bb5fcd2986e284516370e33 100644
--- a/.cwl/cwl-plots/plot.cwl
+++ b/.cwl/cwl-plots/plot.cwl
@@ -1,35 +1,85 @@
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
-class: CommandLineTool
-requirements:
- InitialWorkDirRequirement:
- listing:
- - entryname: plot-cwls.sh
- entry:
- $include: plot-cwls.sh
-
-baseCommand: ["bash", "plot-cwls.sh"]
+class: Workflow
inputs:
- arcRoot:
- type: Directory
- inputBinding:
- position: 1
- cwlPattern:
- type: string
- inputBinding:
- position: 2
- outWflList:
- type: string
- inputBinding:
- position: 3
- outGraphs:
- type: string
- inputBinding:
- position: 4
+ arcRoot:
+ type: Directory
+ cwlPattern:
+ type: string
+ outWflList:
+ type: string
+ outGraphs:
+ type: string
outputs:
- output_files:
- type: File[]
- outputBinding:
- glob: $(inputs.outGraphs)/*.svg
+ outputDir:
+ type: Directory
+ outputSource: collect_files/outDir
+
+steps:
+ plot:
+ run:
+ class: CommandLineTool
+ requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: plot-cwls.sh
+ entry:
+ $include: plot-cwls.sh
+
+ baseCommand: ["bash", "plot-cwls.sh"]
+
+ inputs:
+ arcRoot:
+ type: Directory
+ inputBinding:
+ position: 1
+ cwlPattern:
+ type: string
+ inputBinding:
+ position: 2
+ outWflList:
+ type: string
+ inputBinding:
+ position: 3
+ outGraphs:
+ type: string
+ inputBinding:
+ position: 4
+
+ outputs:
+ output_files:
+ type: File[]
+ outputBinding:
+ glob: $(inputs.outGraphs)/*.svg
+ in:
+ arcRoot: arcRoot
+ cwlPattern: cwlPattern
+ outWflList: outWflList
+ outGraphs: outGraphs
+
+ out: [output_files]
+
+ collect_files:
+ run:
+ class: ExpressionTool
+ requirements:
+ InlineJavascriptRequirement: {}
+ inputs:
+ files: File[]
+ destination: string
+ expression: |
+ ${
+ return {"outDir": {
+ "class": "Directory",
+ "basename": inputs.destination,
+ "listing": inputs.files
+ } };
+ }
+ outputs:
+ outDir: Directory
+ in:
+ files: plot/output_files
+ destination: outGraphs
+ out: [outDir]
diff --git a/.cwl/cwl-plots/runs/deseq2.svg b/.cwl/cwl-plots/runs/deseq2.svg
new file mode 100644
index 0000000000000000000000000000000000000000..29efcbd3c929503f6c29c08d9a688033e46afd86
--- /dev/null
+++ b/.cwl/cwl-plots/runs/deseq2.svg
@@ -0,0 +1,89 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="564pt" height="246pt"
+ viewBox="0.00 0.00 564.00 246.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 242)">
+<title>G</title>
+<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-242 560,-242 560,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-155 8,-230 548,-230 548,-155 8,-155"/>
+<text text-anchor="middle" x="492.92" y="-161.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
+</g>
+<g id="clust2" class="cluster">
+<title>cluster_outputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="214,-8 214,-83 333,-83 333,-8 214,-8"/>
+<text text-anchor="middle" x="273.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- inKallistoResults -->
+<g id="node1" class="node">
+<title>inKallistoResults</title>
+<polygon fill="#94ddf4" stroke="black" points="427.78,-185.5 427.78,-221.5 540.22,-221.5 540.22,-185.5 427.78,-185.5"/>
+<text text-anchor="middle" x="484" y="-199.3" font-family="Times,serif" font-size="14.00">inKallistoResults</text>
+</g>
+<!-- deseq2 -->
+<g id="node5" class="node">
+<title>deseq2</title>
+<ellipse fill="none" stroke="black" cx="273" cy="-129" rx="34.83" ry="18"/>
+<text text-anchor="middle" x="273" y="-124.8" font-family="Times,serif" font-size="14.00">deseq2</text>
+</g>
+<!-- inKallistoResults->deseq2 -->
+<g id="edge1" class="edge">
+<title>inKallistoResults->deseq2</title>
+<path fill="none" stroke="black" d="M465.54,-185.39C453.25,-174.97 436.25,-162.3 419,-155 386.69,-141.33 347.36,-135.13 317.66,-132.32"/>
+<polygon fill="black" stroke="black" points="317.85,-128.82 307.59,-131.46 317.25,-135.8 317.85,-128.82"/>
+</g>
+<!-- inMetadataFactorList -->
+<g id="node2" class="node">
+<title>inMetadataFactorList</title>
+<polygon fill="#94ddf4" stroke="black" points="273.74,-185.5 273.74,-221.5 410.26,-221.5 410.26,-185.5 273.74,-185.5"/>
+<text text-anchor="middle" x="342" y="-199.3" font-family="Times,serif" font-size="14.00">inMetadataFactorList</text>
+</g>
+<!-- inMetadataFactorList->deseq2 -->
+<g id="edge2" class="edge">
+<title>inMetadataFactorList->deseq2</title>
+<path fill="none" stroke="black" d="M325.65,-185.32C316.41,-175.61 304.75,-163.36 294.75,-152.86"/>
+<polygon fill="black" stroke="black" points="297.25,-150.41 287.82,-145.58 292.18,-155.23 297.25,-150.41"/>
+</g>
+<!-- inMetadataFile -->
+<g id="node3" class="node">
+<title>inMetadataFile</title>
+<polygon fill="#94ddf4" stroke="black" points="154.62,-185.5 154.62,-221.5 255.38,-221.5 255.38,-185.5 154.62,-185.5"/>
+<text text-anchor="middle" x="205" y="-199.3" font-family="Times,serif" font-size="14.00">inMetadataFile</text>
+</g>
+<!-- inMetadataFile->deseq2 -->
+<g id="edge3" class="edge">
+<title>inMetadataFile->deseq2</title>
+<path fill="none" stroke="black" d="M221.12,-185.32C230.13,-175.71 241.49,-163.6 251.28,-153.16"/>
+<polygon fill="black" stroke="black" points="254.1,-155.26 258.39,-145.58 249,-150.47 254.1,-155.26"/>
+</g>
+<!-- inMetadataSample -->
+<g id="node4" class="node">
+<title>inMetadataSample</title>
+<polygon fill="#94ddf4" stroke="black" points="15.52,-185.5 15.52,-221.5 136.48,-221.5 136.48,-185.5 15.52,-185.5"/>
+<text text-anchor="middle" x="76" y="-199.3" font-family="Times,serif" font-size="14.00">inMetadataSample</text>
+</g>
+<!-- inMetadataSample->deseq2 -->
+<g id="edge4" class="edge">
+<title>inMetadataSample->deseq2</title>
+<path fill="none" stroke="black" d="M96.47,-185.35C109.78,-175.05 127.97,-162.52 146,-155 172.43,-143.97 204.02,-137.73 229.08,-134.24"/>
+<polygon fill="black" stroke="black" points="229.57,-137.7 239.04,-132.95 228.67,-130.76 229.57,-137.7"/>
+</g>
+<!-- output -->
+<g id="node6" class="node">
+<title>output</title>
+<polygon fill="#94ddf4" stroke="black" points="246,-38.5 246,-74.5 300,-74.5 300,-38.5 246,-38.5"/>
+<text text-anchor="middle" x="272.89" y="-52.3" font-family="Times,serif" font-size="14.00">output</text>
+</g>
+<!-- deseq2->output -->
+<g id="edge5" class="edge">
+<title>deseq2->output</title>
+<path fill="none" stroke="black" d="M273,-110.93C273,-103.17 273,-93.78 273,-85.06"/>
+<polygon fill="black" stroke="black" points="276.5,-84.9 273,-74.9 269.5,-84.9 276.5,-84.9"/>
+</g>
+</g>
+</svg>
diff --git a/.cwl/cwl-plots/runs/fastqc.svg b/.cwl/cwl-plots/runs/fastqc.svg
new file mode 100644
index 0000000000000000000000000000000000000000..485ba4ec8a3c8a5460032d39b3b4419cf03e731a
--- /dev/null
+++ b/.cwl/cwl-plots/runs/fastqc.svg
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="186pt" height="246pt"
+ viewBox="0.00 0.00 186.00 246.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 242)">
+<title>G</title>
+<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-242 182,-242 182,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-155 8,-230 170,-230 170,-155 8,-155"/>
+<text text-anchor="middle" x="114.92" y="-161.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
+</g>
+<g id="clust2" class="cluster">
+<title>cluster_outputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="32,-8 32,-83 151,-83 151,-8 32,-8"/>
+<text text-anchor="middle" x="91.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- fastq -->
+<g id="node1" class="node">
+<title>fastq</title>
+<polygon fill="#94ddf4" stroke="black" points="108,-185.5 108,-221.5 162,-221.5 162,-185.5 108,-185.5"/>
+<text text-anchor="middle" x="134.61" y="-199.3" font-family="Times,serif" font-size="14.00">fastq</text>
+</g>
+<!-- fastqc -->
+<g id="node3" class="node">
+<title>fastqc</title>
+<ellipse fill="none" stroke="black" cx="72" cy="-129" rx="31.45" ry="18"/>
+<text text-anchor="middle" x="72" y="-124.8" font-family="Times,serif" font-size="14.00">fastqc</text>
+</g>
+<!-- fastq->fastqc -->
+<g id="edge1" class="edge">
+<title>fastq->fastqc</title>
+<path fill="none" stroke="black" d="M123.03,-185.22C116.33,-175.95 107.62,-164.51 99,-155 97.98,-153.88 96.92,-152.74 95.83,-151.62"/>
+<polygon fill="black" stroke="black" points="98.03,-148.87 88.44,-144.36 93.12,-153.87 98.03,-148.87"/>
+</g>
+<!-- finaloutdir -->
+<g id="node2" class="node">
+<title>finaloutdir</title>
+<polygon fill="#94ddf4" stroke="black" points="15.83,-185.5 15.83,-221.5 90.17,-221.5 90.17,-185.5 15.83,-185.5"/>
+<text text-anchor="middle" x="53" y="-199.3" font-family="Times,serif" font-size="14.00">finaloutdir</text>
+</g>
+<!-- finaloutdir->fastqc -->
+<g id="edge2" class="edge">
+<title>finaloutdir->fastqc</title>
+<path fill="none" stroke="black" d="M57.5,-185.32C59.73,-176.83 62.46,-166.39 64.96,-156.88"/>
+<polygon fill="black" stroke="black" points="68.38,-157.62 67.53,-147.06 61.61,-155.84 68.38,-157.62"/>
+</g>
+<!-- outdir -->
+<g id="node4" class="node">
+<title>outdir</title>
+<polygon fill="#94ddf4" stroke="black" points="45,-38.5 45,-74.5 99,-74.5 99,-38.5 45,-38.5"/>
+<text text-anchor="middle" x="71.72" y="-52.3" font-family="Times,serif" font-size="14.00">outdir</text>
+</g>
+<!-- fastqc->outdir -->
+<g id="edge3" class="edge">
+<title>fastqc->outdir</title>
+<path fill="none" stroke="black" d="M72,-110.93C72,-103.17 72,-93.78 72,-85.06"/>
+<polygon fill="black" stroke="black" points="75.5,-84.9 72,-74.9 68.5,-84.9 75.5,-84.9"/>
+</g>
+</g>
+</svg>
diff --git a/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg b/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg
new file mode 100644
index 0000000000000000000000000000000000000000..6523ee32fe0a0c45499659ca53496931b0cebf01
--- /dev/null
+++ b/.cwl/cwl-plots/runs/isaSampleToRawDataSeq.svg
@@ -0,0 +1,89 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="416pt" height="246pt"
+ viewBox="0.00 0.00 416.00 246.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 242)">
+<title>G</title>
+<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-242 412,-242 412,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-155 8,-230 400,-230 400,-155 8,-155"/>
+<text text-anchor="middle" x="344.92" y="-161.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
+</g>
+<g id="clust2" class="cluster">
+<title>cluster_outputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="171,-8 171,-83 290,-83 290,-8 171,-8"/>
+<text text-anchor="middle" x="230.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- arcPath -->
+<g id="node1" class="node">
+<title>arcPath</title>
+<polygon fill="#94ddf4" stroke="black" points="334.01,-185.5 334.01,-221.5 391.99,-221.5 391.99,-185.5 334.01,-185.5"/>
+<text text-anchor="middle" x="363" y="-199.3" font-family="Times,serif" font-size="14.00">arcPath</text>
+</g>
+<!-- isaSampleToRawDataSeq -->
+<g id="node5" class="node">
+<title>isaSampleToRawDataSeq</title>
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+</g>
+<!-- arcPath->isaSampleToRawDataSeq -->
+<g id="edge1" class="edge">
+<title>arcPath->isaSampleToRawDataSeq</title>
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new file mode 100644
index 0000000000000000000000000000000000000000..45f69bc844193654382928997d43f78b3e2171f4
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+<text text-anchor="middle" x="377.25" y="-14.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
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+<!-- BootstrapSamples -->
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+<!-- kallisto -->
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+</g>
+<!-- BootstrapSamples->kallisto -->
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+<title>BootstrapSamples->kallisto</title>
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+<!-- FragmentLength->kallisto -->
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+<title>FragmentLength->kallisto</title>
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+<!-- IndexInput->kallisto -->
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+<!-- StandardDeviation->kallisto -->
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+<!-- sampleRecord->kallisto -->
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+<!-- kallisto->finalOut -->
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+<!-- in_kallisto_df->run_shiny -->
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diff --git a/README.md b/README.md
index 813056a360aa436efeb8ca46167109d4f4ce4e54..62ea32b962470601a6064a216c3121ca7983dafa 100644
--- a/README.md
+++ b/README.md
@@ -1,20 +1,11 @@
# Facultative CAM in Talinum
-## Data origin
-
-- see [isa.investigation.xlsx](./isa.investigation.xlsx) for details
-- Adapted from
- > Brilhaus, D., Bräutigam, A., Mettler-Altmann, T., Winter, K., and Weber, A.P.M. (2016). Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in *Talinum triangulare*. Plant Physiology 170: 102–122. <https://doi.org/10.1104/pp.15.01076>
-- [studies/TalinumGenomeDraft](./studies/TalinumGenomeDraft) originates from <https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome>
-
-<!--- Start of automated section -->
-
-# Facultative CAM in Talinum triangulare
+This ARC is based on Brilhaus et al. (2016). <https://doi.org/10.1104/pp.15.01076>. See [isa.investigation.xlsx](./isa.investigation.xlsx) for details.
+The [Talinum Genome Draft](./studies/TalinumGenomeDraft) originates from <https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome>
## Table of Contents
1. [Description](#description)
-1. [Contacts](#contacts)
2. [Publication](#publication)
3. Studies
- [TalinumGenomeDraft](#study--talinumgenomedraft)
@@ -87,16 +78,6 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
| Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets |
| Assay Count | 3 |
-## Contacts
-
-| Names | Email | Address | Affiliation | ORCID |
-| ----- | ----- | ------- | ----------- | ----- |
-| Dominik Brilhaus | <brilhaus@hhu.de> | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0001-9021-3197> |
- | Andrea Bräutigam | <andrea.brauetigam@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-5309-0527> |
- | Tabea Mettler-Altmann | <tabea.mettler@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0002-9161-4889> |
- | Klaus Winter | <winterk@si.edu> | Balboa, Ancón, Republic of Panama | Smithsonian Tropical Research Institute, Panama | |
- | Andreas P M Weber | <aweber@hhu.de> | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | <http://orcid.org/0000-0003-0970-4672> |
-
## Publication
| Meta Data | Description |
@@ -191,5 +172,3 @@ class TalinumGenomeDraft,plant_material,mh-quant-results,mh-quant-report,rna_ext
### Annotation headers
**Parameters**: [Bio entity](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000012),[Biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[Biosource material state](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010009),[Extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[Extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[Internal standard](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010012),[Sample volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010013),[MS sample post-extraction](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000043),[MS sample resuspension](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000044),[MS derivatization](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000052),[MS sample type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000045),[Chromatography instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000046),[Chromatography autosampler model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000047),[Chromatography column type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000053),[Chromatography column model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000048),[mobile phase](http://purl.obolibrary.org/obo/CHMO_0000995),[Chromatography injection volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010014),[Chromatography injection mode](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010015),[Chromatography gradient](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000081),[scan polarity](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000465),[scan window lower limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501),[scan window upper limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000500),[scan rate](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000015),[instrument model](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031),[ionization type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000008),[mass analyzer type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443),[detector type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000026)
-
-<!--- End of automated section -->
\ No newline at end of file
diff --git a/runs/README.md b/runs/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..20bbc21549b15dee5fc8eb4df737766139b0ca97
--- /dev/null
+++ b/runs/README.md
@@ -0,0 +1,3 @@
+# Runs
+
+See [.cwl/README.md](../.cwl/README.md) for more info.
diff --git a/workflows/README.md b/workflows/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..0f64034849e6b184d00c9e016fb085cfbb7bd6e6
--- /dev/null
+++ b/workflows/README.md
@@ -0,0 +1,3 @@
+# Workflows
+
+See [.cwl/README.md](../.cwl/README.md) for more info.