diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e40f2eb6..d1e1401f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -40,14 +40,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:dev # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:dev - name: Install Nextflow uses: nf-core/setup-nextflow@v1 @@ -94,14 +94,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.2 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:dev # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.2 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:dev - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/Dockerfile b/Dockerfile index c13267b3..4f8ce7fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,14 +5,14 @@ LABEL org.opencontainers.image.authors="Gisela Gabernet, Alexander Peltzer, Oska LABEL org.opencontainers.image.licenses=MIT COPY environment.yml / #RUN conda install -c conda-forge mamba -RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.2 && \ +RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-dev && \ mamba clean --all --yes RUN apt-get update -qq && \ apt-get install -y zip procps ghostscript # Add conda installation dir to PATH -ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.2/bin:$PATH +ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-dev/bin:$PATH # Dump the details of the installed packates to a file for posterity -RUN mamba env export --name qbic-pipelines-rnadeseq-2.2 > qbic-pipelines-rnadeseq-2.2.yml +RUN mamba env export --name qbic-pipelines-rnadeseq-dev > qbic-pipelines-rnadeseq-dev.yml # Instruct R processes to use these empty files instead of clashing with a local config RUN touch .Rprofile RUN touch .Renviron diff --git a/environment.yml b/environment.yml index cf3dc64d..cede896c 100644 --- a/environment.yml +++ b/environment.yml @@ -1,7 +1,7 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml # use this to find packages: https://anaconda.org/ -name: qbic-pipelines-rnadeseq-2.2 +name: qbic-pipelines-rnadeseq-dev channels: - bioconda - conda-forge diff --git a/modules/local/report.nf b/modules/local/report.nf index eac509d0..167fceb5 100644 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -1,6 +1,6 @@ process REPORT { - container 'ghcr.io/qbic-pipelines/rnadeseq:2.2' + container 'ghcr.io/qbic-pipelines/rnadeseq:dev' input: path gene_counts diff --git a/nextflow.config b/nextflow.config index 9018f037..21173295 100644 --- a/nextflow.config +++ b/nextflow.config @@ -252,7 +252,7 @@ manifest { description = """Differential gene expression analysis and pathway analysis of RNAseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2' + version = '2.3dev' doi = '' }