Merge remote-tracking branch 'refs/remotes/origin/main'

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.3
+current_version = 0.1.5
 commit = True
 tag = True
 

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
           platforms: linux/amd64
           load: true
           push: false
-          tags: ghcr.io/${{ github.repository }}:0.1.3, ghcr.io/${{ github.repository }}:latest
+          tags: ghcr.io/${{ github.repository }}:0.1.5, ghcr.io/${{ github.repository }}:latest
       - name: 'Install Nextflow'
         uses: stracquadaniolab/[email protected]
       - name: 'Testing Nextflow pipeline with test profile'
@@ -39,4 +39,4 @@ jobs:
           file: containers/Dockerfile
           platforms: linux/amd64
           push: true
-          tags: ghcr.io/${{ github.repository }}:0.1.3, ghcr.io/${{ github.repository }}:latest
+          tags: ghcr.io/${{ github.repository }}:0.1.5, ghcr.io/${{ github.repository }}:latest

.gitignore

@@ -4,4 +4,5 @@ logs/
 .DS_Store
 *.pyc
 .vscode
-.nextflow*
+.nextflow*
+.venv

conf/base.config

@@ -2,7 +2,7 @@
 manifest {
   name = 'enzyme-screening-platform-opentrons'
   description = 'opentrons protocol'
-  version = '0.1.3'
+  version = '0.1.5'
   homePage = 'https://github.com/stracquadaniolab/enzyme-screening-platform-opentrons.git'
   author = 'Martyna Kasprzyk'
   nextflowVersion = '>=20.07.1'
@@ -40,7 +40,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
 
-        process.container = "ghcr.io/stracquadaniolab/enzyme-screening-platform-opentrons:0.1.3"
+        process.container = "ghcr.io/stracquadaniolab/enzyme-screening-platform-opentrons:0.1.5"
     }
 
     singularity {
@@ -51,7 +51,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
 
-        process.container = "docker://ghcr.io/stracquadaniolab/enzyme-screening-platform-opentrons:0.1.3"
+        process.container = "docker://ghcr.io/stracquadaniolab/enzyme-screening-platform-opentrons:0.1.5"
     }
 
     slurm {

containers/Dockerfile

@@ -14,6 +14,7 @@ CMD ["/bin/bash"]
 ## main container
 ARG CONDA_FILE=containers/environment.yml
 FROM base_container
+
 # adding opencontainer labels to link registry to github repository
 LABEL org.opencontainers.image.title="enzyme-screening-platform-opentrons"
 LABEL org.opencontainers.image.description="End-to-end eznyme screening platform for argB."
@@ -22,7 +23,7 @@ LABEL org.opencontainers.image.documentation="https://github.com/stracquadaniola
 LABEL org.opencontainers.image.source="https://github.com/stracquadaniolab/enzyme-screening-platform-opentrons"
 LABEL org.opencontainers.image.vendor="stracquadaniolab"
 LABEL org.opencontainers.image.authors="Martyna Kasprzyk"
-LABEL org.opencontainers.image.revision="v0.1.3"
+LABEL org.opencontainers.image.revision="v0.1.5"
 
 COPY --chown=micromamba:micromamba ${CONDA_FILE} /tmp
 RUN micromamba install -y -n base -f /tmp/`basename ${CONDA_FILE}` && \

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

main.nf

@@ -7,6 +7,7 @@ include { CREATE_LABWARE_CSV as CREATE_LABWARE_CSV_3; VISUALISE_LABWARE as VISUA
 
 workflow {
 
+<<<<<<< HEAD
     // PROTOCOL 1 - TRANSFORMATION
     MAKE_PROTOCOL_1(
         tuple(file("$params.protocol_1_config"), file("$params.protocol_1_data")), 
@@ -67,4 +68,10 @@ workflow {
         VISUALISE_LABWARE_3.out
     )
 
+=======
+    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)
+>>>>>>> refs/remotes/origin/main
 }