From 83587a9bf0c5b049bb00a3d5ce65f639d71ef1ec Mon Sep 17 00:00:00 2001 From: m-kasprzyk Date: Fri, 3 May 2024 20:52:34 +0100 Subject: [PATCH 1/4] 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' From 99b40b387cd30b774a173288044ece4ab630bbee Mon Sep 17 00:00:00 2001 From: m-kasprzyk Date: Fri, 3 May 2024 20:58:06 +0100 Subject: [PATCH 2/4] =?UTF-8?q?Bump=20version:=200.1.3=20=E2=86=92=200.1.4?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- .github/workflows/ci.yml | 4 ++-- conf/base.config | 6 +++--- containers/Dockerfile | 2 +- readme.md | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 363709c..ec934df 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.3 +current_version = 0.1.4 commit = True tag = True diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 56e5272..ca6038f 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/${{ github.repository }}:0.1.4, ghcr.io/${{ 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/${{ github.repository }}:0.1.4, ghcr.io/${{ github.repository }}:latest \ No newline at end of file diff --git a/conf/base.config b/conf/base.config index 6457c5a..27b3029 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 = '0.1.4' 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:0.1.4" } 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:0.1.4" } slurm { diff --git a/containers/Dockerfile b/containers/Dockerfile index c730f4e..92ba72c 100644 --- a/containers/Dockerfile +++ b/containers/Dockerfile @@ -22,7 +22,7 @@ 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="v0.1.4" COPY --chown=micromamba:micromamba ${CONDA_FILE} /tmp RUN micromamba install -y -n base -f /tmp/`basename ${CONDA_FILE}` && \ diff --git a/readme.md b/readme.md index cb41cc5..6398c2f 100644 --- a/readme.md +++ b/readme.md @@ -1,6 +1,6 @@ # protein-expression-opentrons-nf -![](https://img.shields.io/badge/current_version-0.1.3-blue) +![](https://img.shields.io/badge/current_version-0.1.4-blue) ![](https://github.com/stracquadaniolab/protein-expression-opentrons-nf/workflows/build/badge.svg) ## Overview opentrons protocol From 33146f427f2fb97f04bdfc2894efc6374d3bb0da Mon Sep 17 00:00:00 2001 From: m-kasprzyk Date: Fri, 3 May 2024 21:09:27 +0100 Subject: [PATCH 3/4] fixing docker --- .gitignore | 3 ++- containers/Dockerfile | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) 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/containers/Dockerfile b/containers/Dockerfile index 92ba72c..4df2c4b 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." From 76fe3a3b75843d6524fe8e20cf2341a947049d32 Mon Sep 17 00:00:00 2001 From: m-kasprzyk Date: Fri, 3 May 2024 21:09:58 +0100 Subject: [PATCH 4/4] =?UTF-8?q?Bump=20version:=200.1.4=20=E2=86=92=200.1.5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- .github/workflows/ci.yml | 4 ++-- conf/base.config | 6 +++--- containers/Dockerfile | 2 +- readme.md | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index ec934df..9338f5b 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.4 +current_version = 0.1.5 commit = True tag = True diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ca6038f..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 }}:0.1.4, 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 }}:0.1.4, 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/conf/base.config b/conf/base.config index 27b3029..30a37e2 100644 --- a/conf/base.config +++ b/conf/base.config @@ -2,7 +2,7 @@ manifest { name = 'enzyme-screening-platform-opentrons' description = 'opentrons protocol' - version = '0.1.4' + 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:0.1.4" + 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:0.1.4" + process.container = "docker://ghcr.io/stracquadaniolab/enzyme-screening-platform-opentrons:0.1.5" } slurm { diff --git a/containers/Dockerfile b/containers/Dockerfile index 4df2c4b..dc1f20c 100644 --- a/containers/Dockerfile +++ b/containers/Dockerfile @@ -23,7 +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="v0.1.4" +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/readme.md b/readme.md index 6398c2f..3a07acb 100644 --- a/readme.md +++ b/readme.md @@ -1,6 +1,6 @@ # protein-expression-opentrons-nf -![](https://img.shields.io/badge/current_version-0.1.4-blue) +![](https://img.shields.io/badge/current_version-0.1.5-blue) ![](https://github.com/stracquadaniolab/protein-expression-opentrons-nf/workflows/build/badge.svg) ## Overview opentrons protocol