From f7da0ccbf28e9ffc0a7f61db91989e7c151d9300 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 27 Feb 2023 09:35:00 +0100 Subject: [PATCH 1/2] add gitpod nextflow version and use dev container --- .github/RELEASE_CHECKLIST.md | 4 ++-- .gitpod.yml | 2 +- nf_core/gitpod/gitpod.Dockerfile | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md index f2d2591f16..f7cab98c55 100644 --- a/.github/RELEASE_CHECKLIST.md +++ b/.github/RELEASE_CHECKLIST.md @@ -3,7 +3,7 @@ 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9) 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_. 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc) -4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`. +4. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`. 5. Make sure all CI tests are passing! 6. Create a PR from `dev` to `master` 7. Make sure all CI tests are passing again (additional tests are run on PRs to `master`) @@ -19,4 +19,4 @@ 1. Check the automated template synchronisation has been triggered properly. This should automatically open PRs directly to individual pipeline repos with the appropriate changes to update the pipeline template. 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/) 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065) -4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` +4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`. diff --git a/.gitpod.yml b/.gitpod.yml index 263fcc41db..a93e660516 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:latest +image: nfcore/gitpod:dev tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index fa435c3612..417208a20d 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -38,7 +38,7 @@ 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 \ + nextflow=22.10.1 \ nf-core \ nf-test \ black \ From 953f47482295ca66ab9e03982441d2f04bbe9cd9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 27 Feb 2023 09:39:27 +0100 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 67e6ada896..7ca913078b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,8 @@ ### General - `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)). +- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196)) +- Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196)) ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]