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Merged
vagkaratzas merged 2 commits into from
May 12, 2025
Merged

Important! Template update for nf-core/tools v3.2.1 #42

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e7ea1e4
Template update for nf-core/tools version 3.2.1
nf-core-bot Apr 30, 2025
b11c74d
Merge branch 'dev' into nf-core-template-merge-3.2.1
vagkaratzas May 11, 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/denovotranscript' && 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/denovotranscript' && 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/request-action@v2.x
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 @@ -52,12 +31,12 @@ 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/denovotranscript/work-${{ github.sha }}
revision: ${{ steps.revision.outputs.revision }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/denovotranscript/work-${{ steps.revision.outputs.revision }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/denovotranscript/results-${{ github.sha }}"
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/denovotranscript/results-${{ 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:
nextflow_config:
- config_defaults:
- params.ribo_database_manifest
nf_core_version: 3.2.0
nf_core_version: 3.2.1
repository_type: pipeline
template:
author: Avani Bhojwani and Timothy Little
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.3.0dev - [2025-01-31]
## v1.3.0dev - [date]
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@jonasscheid jonasscheid May 11, 2025

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Update changelog

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@vagkaratzas vagkaratzas May 12, 2025

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Uhm, do I need to change something here?

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@vagkaratzas vagkaratzas May 12, 2025

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I guess the date here will be updated when release 1.3.0 is out. Merging like this for now ;)

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@jonasscheid jonasscheid May 12, 2025

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I meant that you could add this PR in the #Changed section of CHANGELOG. By this everyone knows which template version your pipeline supports


- [PR #37](https://github.com/nf-core/denovotranscript/pull/37) - Bump version to 1.3.0dev

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7 changes: 3 additions & 4 deletions assets/multiqc_config.yml
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@@ -1,8 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/tree/dev"
target="_blank">nf-core/denovotranscript</a> analysis pipeline. For information
about how to interpret these results, please see the <a href="https://nf-co.re/denovotranscript/dev/docs/output"
target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/tree/dev" target="_blank">nf-core/denovotranscript</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/denovotranscript/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-denovotranscript-methods-description":
order: -1000
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -297,7 +297,7 @@ manifest {

// Nextflow plugins
plugins {
id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
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