new: added simple protocol compiler to replace bash script. Nextflow …

…to add
stracquadaniolab · Feb 22, 2024 · 7b24cdd · 7b24cdd
1 parent 5b3f154
commit 7b24cdd
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Showing 18 changed files with 535 additions and 317 deletions.
diff --git a/.devcontainer.json b/.devcontainer.json
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,51 @@
+{
+	// workspace setup
+	"name": "enzyme screening platform",
+
+	// setup a container to develop an OT2 protocol
+	"dockerFile": "../containers/Dockerfile",
+	"context": ".",
+
+	// Set *default* container specific settings.json values.
+	// vs set code specific options
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"stkb.rewrap",
+				"christian-kohler.path-intellisense",
+				"streetsidesoftware.code-spell-checker",
+				"aaron-bond.better-comments",
+				"gruntfuggly.todo-tree",
+				"mhutchie.git-graph",
+				"donjayamanne.githistory",
+				"github.vscode-github-actions", 
+				"ms-azuretools.vscode-docker", 
+				"ms-python.python",
+                "ms-python.black-formatter",
+				"njpwerner.autodocstring",
+				"nextflow.nextflow", 
+				"timonwong.shellcheck"
+			],
+			"settings": {
+				"editor.tabSize": 4,
+				"terminal.integrated.defaultProfile.linux": "bash",
+				"terminal.integrated.profiles.linux": {
+					"bash": {
+						"path": "/bin/bash",
+						"icon": "terminal-bash"
+					}
+				},
+				"python.formatting.provider": "none",
+                "source.organizeImports": true,
+				"[python]": {
+                    "editor.defaultFormatter": "ms-python.black-formatter",
+                    "editor.formatOnSave": true,
+                    "editor.codeActionsOnSave": [
+                        "source.organizeImports"
+                    ]
+                }
+			}
+		}
+	}
+
+}
diff --git a/OT2-setup/setup/protocol-templates/spotting-template.py b/OT2-setup/setup/protocol-templates/spotting-template.py
diff --git a/OT2-setup/setup/protocol-templates/transformation-template.py b/OT2-setup/setup/protocol-templates/transformation-template.py
diff --git a/...lo_96_wellplate_200ul_pcr_full_skirt.json → ...lo_96_wellplate_200ul_pcr_full_skirt.json b/...lo_96_wellplate_200ul_pcr_full_skirt.json → ...lo_96_wellplate_200ul_pcr_full_skirt.json
diff --git a/...re/labware/biorad_384_wellplate_50ul.json → ...ts/labware/biorad_384_wellplate_50ul.json b/...re/labware/biorad_384_wellplate_50ul.json → ...ts/labware/biorad_384_wellplate_50ul.json
diff --git a/...abware/biorad_96_wellplate_200ul_pcr.json → ...abware/biorad_96_wellplate_200ul_pcr.json b/...abware/biorad_96_wellplate_200ul_pcr.json → ...abware/biorad_96_wellplate_200ul_pcr.json
diff --git a/...ware/corning_24_wellplate_3.4ml_flat.json → ...ware/corning_24_wellplate_3.4ml_flat.json b/...ware/corning_24_wellplate_3.4ml_flat.json → ...ware/corning_24_wellplate_3.4ml_flat.json
diff --git a/...ware/corning_96_wellplate_360ul_flat.json → ...ware/corning_96_wellplate_360ul_flat.json b/...ware/corning_96_wellplate_360ul_flat.json → ...ware/corning_96_wellplate_360ul_flat.json
diff --git a/...e/labware/nest_96_wellplate_2ml_deep.json → ...s/labware/nest_96_wellplate_2ml_deep.json b/...e/labware/nest_96_wellplate_2ml_deep.json → ...s/labware/nest_96_wellplate_2ml_deep.json
diff --git a/nunc_singlewell_plate_90ml_4x6_grid.json → .../nunc_singlewell_plate_90ml_4x6_grid.json b/nunc_singlewell_plate_90ml_4x6_grid.json → .../nunc_singlewell_plate_90ml_4x6_grid.json
diff --git a/...uberack_falcon_4x50ml_6x15ml_conical.json → ...uberack_falcon_4x50ml_6x15ml_conical.json b/...uberack_falcon_4x50ml_6x15ml_conical.json → ...uberack_falcon_4x50ml_6x15ml_conical.json
diff --git a/...tup/create-labware/labware/petridish.json → assets/labware/petridish.json b/...tup/create-labware/labware/petridish.json → assets/labware/petridish.json
diff --git a/...sascientific_96_wellplate_2.4ml_deep.json → ...sascientific_96_wellplate_2.4ml_deep.json b/...sascientific_96_wellplate_2.4ml_deep.json → ...sascientific_96_wellplate_2.4ml_deep.json