From 1e87880580f9d0dcef37fd1e48d497a85676a92d Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 19 Jul 2024 14:40:54 +0200 Subject: [PATCH 1/2] Changed pipeline version to dev --- CHANGELOG.md | 6 ++++++ Dockerfile | 6 +++--- environment.yml | 2 +- modules/local/report.nf | 2 +- nextflow.config | 2 +- 5 files changed, 12 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c96d268..26aa8ff5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +### Changed + +- [#246](https://github.com/qbic-pipelines/rnadeseq/pull/246) Changed pipeline version to dev + ## 2.3 - Flowering Orchards ### Added diff --git a/Dockerfile b/Dockerfile index 617a13e0..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-2.3 && \ +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-2.3/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-2.3 > qbic-pipelines-rnadeseq-2.3.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 c759c019..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-2.3 +name: qbic-pipelines-rnadeseq-dev channels: - bioconda - conda-forge diff --git a/modules/local/report.nf b/modules/local/report.nf index 05e10831..1df0b399 100644 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -1,6 +1,6 @@ process REPORT { - container 'ghcr.io/qbic-pipelines/rnadeseq:2.3' + container 'ghcr.io/qbic-pipelines/rnadeseq:dev' input: path gene_counts diff --git a/nextflow.config b/nextflow.config index faf95d30..6a66a16f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -276,7 +276,7 @@ manifest { description = """Differential gene expression analysis and pathway analysis of RNAseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3' + version = 'dev' doi = '' } From 02e6f0e882ea8f7fe5a83ad431194acf244b5135 Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Mon, 22 Jul 2024 11:12:25 +0200 Subject: [PATCH 2/2] Update CHANGELOG.md Co-authored-by: Sabrina Krakau --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 26aa8ff5..398e9e04 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- [#246](https://github.com/qbic-pipelines/rnadeseq/pull/246) Changed pipeline version to dev ## 2.3 - Flowering Orchards