From c94b08bf4deed7d46af9592286a390c47a2e4c1d Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 4 May 2023 07:17:28 +0200 Subject: [PATCH 1/2] GitPod base image: Always self-update to the latest version of Nextflow. --- CHANGELOG.md | 2 ++ nf_core/gitpod/gitpod.Dockerfile | 15 +++++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3c0792519..f0940d53b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### General +- GitPod base image: Always self-update to the latest version of Nextflow. + # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27] ### Template diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 417208a20d..252b9bd088 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -38,13 +38,16 @@ RUN conda config --add channels defaults && \ conda config --set channel_priority strict && \ conda install --quiet --yes --name base mamba && \ mamba install --quiet --yes --name base \ - nextflow=22.10.1 \ - nf-core \ - nf-test \ - black \ - prettier \ - pytest-workflow && \ + nextflow \ + nf-core \ + nf-test \ + black \ + prettier \ + pytest-workflow && \ mamba clean --all -f -y +# Update Nextflow +RUN nextflow self-update + # Install nf-core RUN python -m pip install . From 5cd0b867fa06b762762b97530c79aa5915a57a37 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 4 May 2023 07:23:29 +0200 Subject: [PATCH 2/2] GitPod config: Update Nextflow in init. Install pre-commit. --- .gitpod.yml | 1 + CHANGELOG.md | 3 ++- nf_core/gitpod/gitpod.Dockerfile | 1 + nf_core/pipeline-template/.gitpod.yml | 5 +++++ 4 files changed, 9 insertions(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index a93e660516..1cc63b197f 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -5,6 +5,7 @@ tasks: python -m pip install -e . python -m pip install -r requirements-dev.txt pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/CHANGELOG.md b/CHANGELOG.md index f0940d53b9..11bc0e1a69 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,8 @@ ### General -- GitPod base image: Always self-update to the latest version of Nextflow. +- GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency. +- GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config. # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27] diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 252b9bd088..5fce2f055b 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -43,6 +43,7 @@ RUN conda config --add channels defaults && \ nf-test \ black \ prettier \ + pre-commit \ pytest-workflow && \ mamba clean --all -f -y diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 85d95ecc8e..25488dcc08 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack