fixing docker

stracquadaniolab · May 3, 2024 · 83587a9 · 83587a9
1 parent 97ea828
commit 83587a9
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/containers/environment.yml b/containers/environment.yml
@@ -9,8 +9,8 @@ dependencies:
   - opentrons
   - pandas
   - docopt
-  - r-base
-  - r-tidyverse
-  - r-rjson
-  - r-gridExtra
-  - r-png
+  #- r-base
+  #- r-tidyverse
+  #- r-rjson
+  #- r-gridExtra
+  #- r-png
diff --git a/main.nf b/main.nf
@@ -77,6 +77,6 @@ workflow {
 
     CreateProtocol(csv_file_channel, json_file_channel, protocol_template_channel)
     // SimulateProtocol(CreateProtocol.out.protocol)
-    VisualiseLabware(CreateProtocol.out.labware, labware_folder_channel)
-    CreateInstructions(instructions_template_channel, json_file_channel, VisualiseLabware.out.visual)
+    // VisualiseLabware(CreateProtocol.out.labware, labware_folder_channel)
+    // CreateInstructions(instructions_template_channel, json_file_channel, VisualiseLabware.out.visual)
 }
diff --git a/nextflow.config b/nextflow.config
@@ -1,10 +1,10 @@
 params {
-    csvFile = "testdata/induction-data.csv"
-    jsonFile = "testdata/induction-parameters.json"
-    templateFile = "bin/protocol-templates/induction-template.py"
-    instructionsFile = "bin/instructions/induction-instructions.R"
+    csvFile = "testdata/transformation-data.csv"
+    jsonFile = "testdata/transformation-parameters.json"
+    templateFile = "bin/protocol-templates/transformation-template.py"
+    instructionsFile = "bin/instructions/transformation-instructions.R"
     labwareFolder = "testdata/labware"
     resultsDir = "./results"
 }
 
-includeCongif = 'conf/base.config'
+includeConfig = 'conf/base.config'