From 3f09a86cebbe27f3dbfefb55eb84fc7d9a76dca4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 14 Oct 2025 16:28:08 +0200 Subject: [PATCH 1/3] template: fix launch action --- .../.github/workflows/awsfulltest.yml | 12 ++++++------ .../pipeline-template/.github/workflows/awstest.yml | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index 975be1d4dd..83dc64ab06 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -28,15 +28,15 @@ jobs: # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %} + workdir: s3://${{ vars.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %} parameters: | { "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}", - "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}" + "outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}" } profiles: test_full @@ -44,5 +44,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml index 46ec661a12..515b0700e8 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -14,14 +14,14 @@ jobs: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %} + workdir: s3://${{ vars.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %} parameters: | { - "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}" + "outdir": "s3://{% raw %}${{ vars.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}" } profiles: test @@ -29,5 +29,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json From 6afd4a997d1b53234c20bc2706cb0822582913a2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 14 Oct 2025 14:29:58 +0000 Subject: [PATCH 2/3] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 67a6e4d70a..402079b1c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ - Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756)) - Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781)) - update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788)) +- fix launch action ([#3827](https://github.com/nf-core/tools/pull/3827)) ### Linting From e2413b8578eef9598ccb8b6c643f4b55bd441ff0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 14 Oct 2025 16:32:42 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 402079b1c4..a8a6c012a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ - Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756)) - Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781)) - update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788)) -- fix launch action ([#3827](https://github.com/nf-core/tools/pull/3827)) +- fix AWS tests launch action ([#3827](https://github.com/nf-core/tools/pull/3827)) ### Linting