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Commit 90d9fbae authored by Dominik Brilhaus's avatar Dominik Brilhaus
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Merge branch 'workflow-figure' into 'main'

Workflow figure

See merge request brilator/samplearc_rnaseq!12
parents 20a773c6 eae9cc49
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...@@ -8,3 +8,7 @@ This is a minimal example ARC packaging an mRNA-Seq dataset with metadata and co ...@@ -8,3 +8,7 @@ This is a minimal example ARC packaging an mRNA-Seq dataset with metadata and co
- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details. - see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details.
- Published under: <https://doi.org/10.1104/pp.15.01076> - Published under: <https://doi.org/10.1104/pp.15.01076>
## Workflow overview
![](_workflow_scheme/workflow-scheme.drawio.png)
\ No newline at end of file
# Small helper to auto-create an import for draw.io
folder | fill | stroke | shape
-------|------|--------|------
runs | #C21F3A | #2D3E69 | ellipse
assays | #FFC000 | #2D3E68 | rectangle
studies | #B4CE82 | #2D3E50 | rectangle
workflows | #4FB3D9 | #2D3E57 | rhombus
```bash
find runs -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"runs", "#C21F3A", "#2D3E69", "ellipse"}' | tr ' ' ',' > tmp.runs.columns.csv
find assays -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"assays", "#FFC000", "#2D3E69", "rectangle"}' | tr ' ' ',' > tmp.assays.columns.csv
find studies -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"studies", "#B4CE82", "#2D3E50", "rectangle"}' | tr ' ' ',' > tmp.studies.columns.csv
find workflows -mindepth 1 -maxdepth 1 -type d | awk '{print $1,"workflows", "#4FB3D9", "#2D3E57", "rhombus"}' | tr ' ' ',' > tmp.workflows.columns.csv
## append rwo number
cat tmp.*.columns.csv | awk -F',' '{$0=$0","NR} 1' > tmp_drawioimport.csv
awk 'BEGIN{print "step,folder,fill,stroke,shape,id"} {print}' tmp_drawioimport.csv > drawioimport.csv
cat _workflow_scheme/drawioimport_header drawioimport.csv > drawioimport_ready
mv drawioimport* _workflow_scheme
rm tmp*
```
\ No newline at end of file
step,folder,fill,stroke,shape,id
assays/Talinum_RNASeq_minimal,assays,#FFC000,#2D3E69,rectangle,1
runs/shiny_prep,runs,#C21F3A,#2D3E69,ellipse,2
runs/kallisto_quant,runs,#C21F3A,#2D3E69,ellipse,3
runs/merged_isa_metadata,runs,#C21F3A,#2D3E69,ellipse,4
runs/kallisto_collect,runs,#C21F3A,#2D3E69,ellipse,5
runs/kallisto_index,runs,#C21F3A,#2D3E69,ellipse,6
runs/kallisto_sleuth,runs,#C21F3A,#2D3E69,ellipse,7
studies/TalinumGenomeDraft,studies,#B4CE82,#2D3E50,rectangle,8
studies/TalinumFacultativeCAM,studies,#B4CE82,#2D3E50,rectangle,9
workflows/merge_isa_metadata,workflows,#4FB3D9,#2D3E57,rhombus,10
workflows/shiny_prep,workflows,#4FB3D9,#2D3E57,rhombus,11
workflows/kallisto_quant,workflows,#4FB3D9,#2D3E57,rhombus,12
workflows/kallisto_collect,workflows,#4FB3D9,#2D3E57,rhombus,13
workflows/kallisto_index,workflows,#4FB3D9,#2D3E57,rhombus,14
workflows/kallisto_sleuth,workflows,#4FB3D9,#2D3E57,rhombus,15
## Hello World
# label: %step%
# style: shape=%shape%;fillColor=%fill%;strokeColor=%stroke%;
# namespace: csvimport-
# width: auto
# height: auto
# padding: 15
# ignore: id,shape,fill,stroke,folder
# nodespacing: 40
# levelspacing: 100
# edgespacing: 40
# layout: auto
## CSV starts under this line
## Hello World
# label: %step%
# style: shape=%shape%;fillColor=%fill%;strokeColor=%stroke%;
# namespace: csvimport-
# width: auto
# height: auto
# padding: 15
# ignore: id,shape,fill,stroke,folder
# nodespacing: 40
# levelspacing: 100
# edgespacing: 40
# layout: auto
## CSV starts under this line
step,folder,fill,stroke,shape,id
assays/Talinum_RNASeq_minimal,assays,#FFC000,#2D3E69,rectangle,1
runs/shiny_prep,runs,#C21F3A,#2D3E69,ellipse,2
runs/kallisto_quant,runs,#C21F3A,#2D3E69,ellipse,3
runs/merged_isa_metadata,runs,#C21F3A,#2D3E69,ellipse,4
runs/kallisto_collect,runs,#C21F3A,#2D3E69,ellipse,5
runs/kallisto_index,runs,#C21F3A,#2D3E69,ellipse,6
runs/kallisto_sleuth,runs,#C21F3A,#2D3E69,ellipse,7
studies/TalinumGenomeDraft,studies,#B4CE82,#2D3E50,rectangle,8
studies/TalinumFacultativeCAM,studies,#B4CE82,#2D3E50,rectangle,9
workflows/merge_isa_metadata,workflows,#4FB3D9,#2D3E57,rhombus,10
workflows/shiny_prep,workflows,#4FB3D9,#2D3E57,rhombus,11
workflows/kallisto_quant,workflows,#4FB3D9,#2D3E57,rhombus,12
workflows/kallisto_collect,workflows,#4FB3D9,#2D3E57,rhombus,13
workflows/kallisto_index,workflows,#4FB3D9,#2D3E57,rhombus,14
workflows/kallisto_sleuth,workflows,#4FB3D9,#2D3E57,rhombus,15
_workflow_scheme/workflow-scheme.drawio.png

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