diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 363709c..9338f5b 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.3 +current_version = 0.1.5 commit = True tag = True diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 56e5272..99b4e75 100644 --- a/.github/workflows/ci.yml +++ b/.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/gh-action-setup-nextflow@v0.2.0 - 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 \ No newline at end of file + tags: ghcr.io/${{ github.repository }}:0.1.5, ghcr.io/${{ github.repository }}:latest \ No newline at end of file diff --git a/.gitignore b/.gitignore index a7bfdd7..23d8f7c 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,5 @@ logs/ .DS_Store *.pyc .vscode -.nextflow* \ No newline at end of file +.nextflow* +.venv \ No newline at end of file diff --git a/conf/base.config b/conf/base.config index b09ffb5..dd4c068 100644 --- a/conf/base.config +++ b/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 { diff --git a/containers/Dockerfile b/containers/Dockerfile index c730f4e..dc1f20c 100644 --- a/containers/Dockerfile +++ b/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 ${CONDA_FILE}` && \ diff --git a/containers/environment.yml b/containers/environment.yml index 56aa8d1..708b355 100644 --- a/containers/environment.yml +++ b/containers/environment.yml @@ -9,8 +9,8 @@ dependencies: - opentrons - pandas - docopt - - r-base - - r-tidyverse - - r-rjson - - r-gridExtra - - r-png + #- r-base + #- r-tidyverse + #- r-rjson + #- r-gridExtra + #- r-png diff --git a/main.nf b/main.nf index 58a2ad7..0360e39 100644 --- a/main.nf +++ b/main.nf @@ -7,6 +7,7 @@ include { CREATE_LABWARE_CSV as CREATE_LABWARE_CSV_3; VISUALISE_LABWARE as VISUA workflow { +<<<<<<< HEAD // PROTOCOL 1 - TRANSFORMATION MAKE_PROTOCOL_1( tuple(file("$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 } \ No newline at end of file