From 7a5f3ca8c3be0e4f8b3f397774b0739eb7e3e71d Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Thu, 14 Nov 2024 16:24:50 +0100
Subject: [PATCH] finalize violas cwl

---
 public/violas-cwl.zip                         | Bin 0 -> 3950 bytes
 .../docs/guides/arc-cwl-wrap-script.mdx       |  98 +++++++++++-------
 2 files changed, 60 insertions(+), 38 deletions(-)
 create mode 100644 public/violas-cwl.zip

diff --git a/public/violas-cwl.zip b/public/violas-cwl.zip
new file mode 100644
index 0000000000000000000000000000000000000000..4236fca09fc5df679165ca05b674698a8575a32e
GIT binary patch
literal 3950
zcmbtW3pkW%8=i5<F^A0<HI$iAX`M#Ih%z%0nV7L+DdikF3>7&<qOsJ-Dw|&k?U==O
z5X#blwM1KNvN|Xkr}alDsRpax{NGDoGsD#OU;pF!yz>p${k-peKkxJ0bgHD38UjRK
zEW=~=!-roA2yMiHJ>j7~`wje}LycUwEk?+MNSg(QLJwG@ViXWaDIOAmm<6EE0?8s|
zMS!F<5C}C<Aj3^AUM`X0`vN{90yHs*qdCSI^#m1LK2wcsYPcpLr6wt*N6OP%TJ?|3
zn{bq?KNHb*_-sB!<;RY&3SWNKMf9HCXF25?7J0M$rjSI0^vS(V+S0d|c(kfN*Ub&9
z{CPMyCZFsZmLZwZQ8@INwwKZ+U0Y`Ja6{hm28t|}IjNPst)=Ndir8B#bV`-;l_GOP
z(*q;97xrE)mh4)Ed9!wXvBJ|f@O_JIb4R>JcjySc1$wvsI{-VgI7<gT!AI@l@hNHM
zP2&S`*Xk}|V{k7kYcT~a*W%H&L|Ol#`iP8!`2cK~pnXfj6G^Aa$YvD}x%WYo1E$1t
z7z6!v1;nA3mm}GR=HhN7q>7=Jcsj!u3gqXF@(c9#^&WHF>NckAmPS7;k*OiMS_OkF
z$EX~cM3Gt$F1^}yhb4*MF{Q|-QG}g?U`H~t3Tbu3b<iHbKIV1^eL$EpM9T#ws&aJr
zzL4Fa;nDl&3TNQ;y1*CE16Hwx10c=jL8^#C?u%l4KpTWm;72SPC_^J5G(hfhQ8d8@
zMH%dbu;FJO_GpfyQv*R|bKsxa`ceHWsYcZ#^oS$MkYt3|^YwN6zqAK8dZr$UKr`B^
z-=J_7_5n5**3v3=abCCTD0D8t^-UF>QT4#B)%o`%A(>45y@y4NF}Jh%{(+lO^L54k
z{dt<k6V&bP=Ud-L<s_D@S^SW8rE#t4rS!b`q77&0Y5`hzH~KP4Uv+Z}tQoiCTxH${
zKW=#VtRN9%>#R0l<#Xcna`VNu&Q6)t*2Ip6yd2fmo_Io2y%H~C_3pRLJ(^}^DOw}F
zPU(&;=Xin}7i|>kBQxz)Q^9_ZS%t&2@^2IjC)zsS)40d7H7>rKtc}gDEDcwlMl##a
z{z)aRvR1e}X!+7xIoh{IR`+gshXg2%^!IWON=V`21v&~d58kyt#e7hJPh^-+#9WEM
zq=R)H@q&9{GEdZ{qR_J?BC2N}1P4F!U`KPvKu@T_XnVY9qGs13Slqg8LvnFQ`y+!m
ztSbGe<4>MUg|{mD7HH#{6t<~-*L}+KEst1#m7CnD=V=_?n%$^ThEQa$v>K@^duKoR
zhA`=uA#WZOaa2Y>x-}}2`OMC}=a=U9Lpx?B8vAdy3}64DH*=g}mHXJW;f`Cw3D>-U
zSdZsBnX$WmE%iE6b)kUG+Q80jJfO~-NMy5hkBt{+>YA(%U3QGEiS<c{xLVv9<daA#
z-r=V|8bqsVtFLA{?XlSb^(02&wIDf`a&NAABWr9@FN1e5p@Mx@G0@p;gx}u#x0mw|
ziRqjt`nf$<v<Fpr+aFgB|AB}wx8tj1-fFH_h<|7Kv_0(Vaw)X|`b|loE3Iq?N_~N@
z!sG*8HN}wsK~e)qi8)ze?!h{be}SyR71IahT`h_%xT|o*d{_-5VrQoasF`QbBc^u3
z=$0Xn$lP~&N>OPx$AfN!$oq$+a{Sl)<~hQ`<2*K>)SB*|&@?v)!%M}*)9zG1N|iD&
zLv8MP;#MEu<xwzF5)>raxD>;1*DO>~F2i0t_x4`7=EXg-ga>(rt88C8Xxt#R_i8C;
zyLIO6KJB}i|N166#Kq*MSvL26oATQV{sE`e64}3<*ut)7p1W2cpN<L`xnikmkyFI}
zQMcwH&0?~MNQgbJ{tlP#c*EU^r^mB@rtWleeQ0CbgRH4@>8#a>cZ#lRO1)pIuIyh}
zy7hDgx%pI8UI@Fz=fS>yqxOufg!}taf5BgC;d>~?jk^u#*JK&rV-8!E22^#lU((gF
zPLx5r{mc6+RFjY6lUJ{pc9~!EDm{<UfX>q<jFP1g-+*)RYRE_+5NrNP4OkyT$SC}i
z9>?kBP7Nf*u2*_neJG~R%?B`Qu9RdY`YEKb=Qnzl)syv8rLHsi)NdTN8J9gdbg1>!
z)Hv?@zBkE4JFZP^nahgPZF;9(ERMt8UdFo;TIvw8$yDESCx*LGwg0Kb1*=20<L-Ew
zHhFLP+l_Wbq^4R6{uF6uAlkqH>3)*rIaE93E;nY7yKLRaedbeBkM`xx8uWx<WN8`|
zQ}w*Fcvw#{HFBy{-<k9LbqpIjnRcF#e4Dh4n`<_r+09MYu~yr=B-Ot)NJmNaQBhfS
zOqXH?rBi1GwW6bHLw|mZ<=w}`E!~5MET~y4UAL6rFJ7<1tIBOGpTU}Zd$)1SFHDyo
zX+jEIe<~{FyE{><ri0lJ%z+N3!4@=CNCUvOKnLObmH^#1yr>Sd%})5f1&8|@#)i!)
z@R@68n{F)6B&cmVNIS7aCt*7_&&;sXu+Xw3Q~x9%A9FA(OtWYycWe>GVRs+RD+fP4
zG-~N`Wm8(r65j9pjpuUBA6<Xy5OFm3?lCJXiHQ_SiPN%4e}|*NXp0+Vm*2H};=ihS
zBI`(GfO9o3YVHn%b`Ew=ry?cPBtPvnp?{f;Q8HMBJkCd-_(|tE2Ml{pVMhhLCmful
zEuz4pg93J;Vw@<vbvT2tBLdD04o=c>B;x<|X>c+CD$ZoV$wtXWP_+p01mD6hv0MTv
z#F;KZie%9gUueMudVt0*Y!ZM8gM*WFUld(%08wQ=>kI@Z5gsBS2e2J*jFKIsK0y{d
zQa&~=INgG2B{&winZh#?*bq24Nk56E`rk~6u>8Ue0KkKR3&$uKw@Bnf3);c#fj-j*
z;7qVt79Iv*0K>saiWki!&<W=5%g6Ejq{5vK%o#X1N%FEH$6J^b{^m=jj&NGQs&Hch
kZ50kq(n&dyv<q1M!X`_nN<*X}5Q@;xOQ;@#<-yy30r%?|Qvd(}

literal 0
HcmV?d00001

diff --git a/src/content/docs/guides/arc-cwl-wrap-script.mdx b/src/content/docs/guides/arc-cwl-wrap-script.mdx
index 9cba97a02..737ef2cd7 100644
--- a/src/content/docs/guides/arc-cwl-wrap-script.mdx
+++ b/src/content/docs/guides/arc-cwl-wrap-script.mdx
@@ -4,11 +4,9 @@ lastUpdated: 2024-11-14
 authors:
   - dominik-brilhaus
 sidebar:
-  order: 4
   badge:
-    text: wip
-    variant: caution
-draft: true
+    text: new
+    variant: tip
 ---
 
 import { FileTree } from '@astrojs/starlight/components';
@@ -17,34 +15,25 @@ import { Tabs, TabItem } from '@astrojs/starlight/components';
 import ViolasARCFinal from '@components/mdx/ViolasARC-final.mdx'
 import Mermaid from '@components/mdx/Mermaid.astro'
 
-:::note
-This builds on the ARC created in the [Start here](/nfdi4plants.knowledgebase/start-here/)
+Here we wrap a minimal example script into a [CWL](/nfdi4plants.knowledgebase/CWL) document. We use a python script (`heatmap.py`), that creates a heatmap file (`heatmap.svg`) based on an input table containing sugar abundance assay data (`sugar_result.csv`).
+Wrappig the script in CWL makes it reusable in another ARC to generate the same type of heatmap based on another input table. For more details, checkout the [CWL](/nfdi4plants.knowledgebase/CWL)
 
-<details>
-<summary>Click here to see what the ARC looks like</summary>
-
-<ViolasARCFinal />
 
-</details>
+## Example Data
 
-You can also download the ARC (e.g. via [ARCitect](/nfdi4plants.knowledgebase/arcitect)) from the [DataHUB](https://git.nfdi4plants.org/training/AthalianaColdStressSugar).
+This guide builds on the ARC created in the [Start here](/nfdi4plants.knowledgebase/start-here/) guide. 
+If you have not yet followed the guide, you can download the ARC (e.g. via [ARCitect](/nfdi4plants.knowledgebase/arcitect)) from the [DataHUB](https://git.nfdi4plants.org/training/AthalianaColdStressSugar).
 
-:::
-
-## Scripts and CWL files
+<details>
+<summary>This is what the ARC looks like</summary>
 
-We generate the following three files and place them in the ARC.
+<ViolasARCFinal />
 
-<div class="overflow-x-auto">
-          <div class="min-w-[800px]" >
+</details>
 
-File name   | Description                                   | Location in the ARC
----         | ---                                           | ---
-`heatmap.py`  | Script used for data analysis | `workflows/heatmap/heatmap.py`
-`workflow.cwl`  | CWL document wrapping the `heatmap.py` | `workflows/heatmap/workflow.cwl`
-`job.yml`  | Yaml providing the parameters for `workflow.cwl` | `runs/heatmap-run/job.yml`
+## Isolate run parameters and workflow
 
-</div></div>
+We add the following three files to the ARC. You can <a href="/nfdi4plants.knowledgebase/violas-cwl.zip">**download the files here**</a>. 
 
 <Tabs syncKey="os">
 <TabItem label="heatmap.py" icon='seti:python'>
@@ -121,18 +110,47 @@ FigureFileName: heatmap
 </TabItem>
 </Tabs>
 
-## Isolate run parameters and workflow 
+<Mermaid>
+
+```mermaid
+flowchart LR
+
+subgraph "workflow.cwl"
+  py@{ shape: doc, label: "heatmap.py" }
+end
+
+sugar_result.csv -.- job.yml --o workflow.cwl--> heatmap.svg
+```
+
+</Mermaid>
+
+Briefly summarized,
+
+- the `heatmap.py` is the example data analysis script, which creates a heatmap based on a CSV table input
+- the `workflow.cwl` is a CWL document binds the `heatmap.py`
+  - It requires two `inputs`
+    1. `MeasurementTableCSV`: the file name of the CSV table
+    2. `FigureFileName`: how the user wants to name the output file
+  - And it generates one `output`: an `.svg` file named according to `FigureFileName`
+- the `job.yml` provides the required `input` parameters for `workflow.cwl`
+  - the relative path to the CSV table input: `sugar_result.csv`
+  - the desired file name: `heatmap`
+
+## Using the workflow in your ARC
 
 <Steps>
 
+1. Open the [example ARC](#example-data)
 1. Add a folder "heatmap" to `workflows`
-1. Add the `workflow.cwl` to `workflows/heatmap`
-1. Add the `heatmap.py` to `workflows/heatmap`
+   - Import `workflow.cwl` into `workflows/heatmap`
+   - Import `heatmap.py` into `workflows/heatmap`
 2. Add a folder "heatmap-run" to `runs` 
-2. Add the `job.yml` to `runs/heatmap-run`
+   - Import `job.yml` into `runs/heatmap-run`
 
 </Steps>
 
+The ARC should now look like this:
+
 <FileTree>
 - assays
   - SugarMeasurement
@@ -151,19 +169,23 @@ FigureFileName: heatmap
     - **workflow.cwl**
 </FileTree>
 
-## Execute the run
 
+<Steps>
 
-<Mermaid>
-
-```mermaid
-flowchart TD
+3. In the ARC, navigate to the `heatmap-run` folder:
 
-heatmap.py --o CWL
+    ```bash
+    cd runs/heatmap-run
+    ```
 
-sugar_result.csv ===CWL@{ shape: doc, label: "workflow.cwl" }==> heatmap.svg
+4. Use the `cwltool` to run the workflow:
 
-job.yml --o CWL
-```
+    ```bash
+    cwltool ../../workflows/heatmap job.yml
+    ```
+    
+    :::note[CWL]
+    This assumes that [cwltool](/nfdi4plants.knowledgebase/cwl/cwl-runner-installation) is installed on your system.
+    :::
 
-</Mermaid>
\ No newline at end of file
+</Steps>