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Important! Template update for nf-core/tools v3.2.1 #25

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Merged
Felix-Kummer merged 3 commits into from
May 27, 2025
Merged

Important! Template update for nf-core/tools v3.2.1 #25

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54d6c77
Template update for nf-core/tools version 3.2.1
nf-core-bot Apr 30, 2025
487b469
Merge branch 'dev' into nf-core-template-merge-3.2.1
Felix-Kummer May 27, 2025
7ae5e95
Reset nf-schema version
Felix-Kummer May 27, 2025
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41 changes: 10 additions & 31 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -4,44 +4,23 @@ name: nf-core AWS full size tests
# It runs the -profile 'test_full' on AWS batch

on:
pull_request:
branches:
- main
- master
workflow_dispatch:
pull_request_review:
types: [submitted]
release:
types: [published]

jobs:
run-platform:
name: Run AWS full tests
# run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
if: github.repository == 'nf-core/rangeland' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
if: github.repository == 'nf-core/rangeland' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
steps:
- name: Get PR reviews
uses: octokit/[email protected]
if: github.event_name != 'workflow_dispatch'
id: check_approvals
continue-on-error: true
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

- name: Check for approvals
if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
run: |
echo "No review approvals found. At least 2 approvals are required to run this action automatically."
exit 1

- name: Check for enough approvals (>=2)
id: test_variables
if: github.event_name != 'workflow_dispatch'
- name: Set revision variable
id: revision
run: |
JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"

- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
Expand All @@ -51,12 +30,12 @@ jobs:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rangeland/work-${{ github.sha }}
revision: ${{ steps.revision.outputs.revision }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rangeland/work-${{ steps.revision.outputs.revision }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rangeland/results-${{ github.sha }}"
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rangeland/results-${{ steps.revision.outputs.revision }}"
}
profiles: test_full

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1 change: 1 addition & 0 deletions .github/workflows/ci.yml
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Expand Up @@ -83,5 +83,6 @@ jobs:
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -2,7 +2,7 @@ lint:
files_exist:
- conf/igenomes.config
- conf/igenomes_ignored.config
nf_core_version: 3.2.0
nf_core_version: 3.2.1
repository_type: pipeline
template:
author: Fabian Lehmann, David Frantz, Felix Kummer
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