From 83587a9bf0c5b049bb00a3d5ce65f639d71ef1ec Mon Sep 17 00:00:00 2001
From: m-kasprzyk <mn.kasprzyk@gmail.com>
Date: Fri, 3 May 2024 20:52:34 +0100
Subject: [PATCH] fixing docker

---
 containers/environment.yml | 10 +++++-----
 main.nf                    |  4 ++--
 nextflow.config            | 10 +++++-----
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/containers/environment.yml b/containers/environment.yml
index 56aa8d1..708b355 100644
--- 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
index 8e31e81..c727b2c 100644
--- 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)
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index bcc7430..5c3cac8 100644
--- 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'