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Update samshee

Update samshee #15

name: nf-core template version comment
# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
# It posts a comment to the PR, even if it comes from a fork.
on: pull_request_target
jobs:
template_version:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
ref: ${{ github.event.pull_request.head.sha }}
- name: Read template version from .nf-core.yml
uses: nichmor/[email protected]
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml
- name: Install nf-core
run: |
python -m pip install --upgrade pip
pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
- name: Check nf-core outdated
id: nf_core_outdated
run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
- name: Post nf-core template version comment
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
if: |
contains(env.OUTPUT, 'nf-core')
with:
repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
allow-repeats: false
message: |
> [!WARNING]
> Newer version of the nf-core template is available.
>
> Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
> Please update your pipeline to the latest version.
>
> For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
#