diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 1bd2e27fb0..8fdd2bd7e1 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -33,7 +33,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 46152d92a7..654d248f79 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -23,7 +23,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: # Get the repo code diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 8f3c5fdb47..7cff154a08 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -23,7 +23,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - uses: actions/checkout@v3 diff --git a/CHANGELOG.md b/CHANGELOG.md index f67548af4c..3de182d7af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,8 @@ - Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/)) - Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306)) - Add ability to specify custom registry for linting modules, defaults to quay.io ([#2313](https://github.com/nf-core/tools/pull/2313)) +- Add `singularity.registry = 'quay.io'` in pipeline template +- Bump minimum required NF version in pipeline template from `22.10.1` -> `23.04.0` ### Download diff --git a/nf_core/lint/readme.py b/nf_core/lint/readme.py index ae5c542837..55060442b1 100644 --- a/nf_core/lint/readme.py +++ b/nf_core/lint/readme.py @@ -36,7 +36,7 @@ def readme(self): if "nextflow_badge" not in ignore_configs: # Check that there is a readme badge showing the minimum required version of Nextflow - # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) + # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) # and that it has the correct version nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)" match = re.search(nf_badge_re, content) diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml index f93cd55d59..063690f29f 100644 --- a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index bf3dc36bc5..521f3e664a 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 5ac65123ed..e66746dcd5 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -10,7 +10,7 @@ {%- if github_badges -%} [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index c8bd1dca06..e329b3e6fe 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -179,8 +179,9 @@ profiles { // Set default registry for Docker and Podman independent of -profile // Will not be used unless Docker / Podman are enabled // Set to your registry if you have a mirror of containers -docker.registry = 'quay.io' -podman.registry = 'quay.io' +singularity.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' // Nextflow plugins plugins { @@ -234,7 +235,7 @@ manifest { homePage = 'https://github.com/{{ name }}' description = """{{ description }}""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '{{ version }}' doi = '' }