diff --git a/README.md b/README.md index 93a63c898477a11064ee7aeb1cebf36fd00fb88e..935e079765989b548e6aa75bf62d89f4828a5863 100644 --- a/README.md +++ b/README.md @@ -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. - Published under: <https://doi.org/10.1104/pp.15.01076> + +## Workflow overview + + \ No newline at end of file diff --git a/_workflow_scheme/README.md b/_workflow_scheme/README.md new file mode 100644 index 0000000000000000000000000000000000000000..79e5ebf37c5aea743071d8e9ead35c167f065022 --- /dev/null +++ b/_workflow_scheme/README.md @@ -0,0 +1,31 @@ + +# 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 diff --git a/_workflow_scheme/drawioimport.csv b/_workflow_scheme/drawioimport.csv new file mode 100644 index 0000000000000000000000000000000000000000..a78b3fcb1f2a3a97e4b939c7976932a073473c70 --- /dev/null +++ b/_workflow_scheme/drawioimport.csv @@ -0,0 +1,16 @@ +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 diff --git a/_workflow_scheme/drawioimport_header b/_workflow_scheme/drawioimport_header new file mode 100644 index 0000000000000000000000000000000000000000..5365f3e9ec0b5056e21f3853b15ea01dec83e178 --- /dev/null +++ b/_workflow_scheme/drawioimport_header @@ -0,0 +1,13 @@ +## 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 diff --git a/_workflow_scheme/drawioimport_ready b/_workflow_scheme/drawioimport_ready new file mode 100644 index 0000000000000000000000000000000000000000..206eeca99f364715dd5fefca5497e6853fd03f31 --- /dev/null +++ b/_workflow_scheme/drawioimport_ready @@ -0,0 +1,29 @@ +## 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 diff --git a/_workflow_scheme/workflow-scheme.drawio.png b/_workflow_scheme/workflow-scheme.drawio.png new file mode 100644 index 0000000000000000000000000000000000000000..d659d714d2dc8035632444eded6d349f71775b88 Binary files /dev/null and b/_workflow_scheme/workflow-scheme.drawio.png differ