From 83533409da603c1dca959296c63bbd510ff48b8a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 6 Jun 2023 10:21:30 +0000 Subject: [PATCH 1/5] Update seqeralabs/action-tower-launch to v1.2.4 - Updates the Github action to v1.2.4 - Adds specific revision which no longer defaults to github.sha - Saves the JSON log created per pipeline as artifact --- CHANGELOG.md | 1 + .../pipeline-template/.github/workflows/awsfulltest.yml | 8 ++++++-- nf_core/pipeline-template/.github/workflows/awstest.yml | 8 ++++++-- 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2deeef5f66..a0584f3e3a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287) - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291)) - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298)) +- Updates seqeralabs/action-tower-launch to v1.2.4 ### Download diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index 9511ea57be..de2fb535a5 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v1.2.4 # TODO nf-core: You can customise AWS full pipeline tests as required # 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 {%- raw %} @@ -22,13 +22,17 @@ 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 }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %} parameters: | { "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}" } profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + 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 6e1fd8c92a..6e5a9a9e42 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action {%- raw %} - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v1.2.4 with: 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 }}{% 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 %}" } profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json From 410db78bf8fdddb8302256a5c08a5bbb5da60fe6 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 6 Jun 2023 15:33:47 +0000 Subject: [PATCH 2/5] Update action to v2.0.0 (breaking change) --- CHANGELOG.md | 2 +- nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +- nf_core/pipeline-template/.github/workflows/awstest.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a0584f3e3a..8a1fb5ae28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287) - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291)) - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298)) -- Updates seqeralabs/action-tower-launch to v1.2.4 +- Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301)) ### Download diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index de2fb535a5..ebad007191 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1.2.4 + uses: seqeralabs/action-tower-launch@v2.0.0 # TODO nf-core: You can customise AWS full pipeline tests as required # 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 {%- raw %} diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml index 6e5a9a9e42..8819b7cca0 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action {%- raw %} - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1.2.4 + uses: seqeralabs/action-tower-launch@v2.0.0 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} From e40580ba71445049caa786fb5b7d4dd639c8713b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 8 Jun 2023 08:59:02 +0000 Subject: [PATCH 3/5] Reduce to shortened version of action-tower-launch version --- nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +- nf_core/pipeline-template/.github/workflows/awstest.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index ebad007191..1d5c53bda9 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2.0.0 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # 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 {%- raw %} diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml index 8819b7cca0..9a0bf4afbc 100644 --- a/nf_core/pipeline-template/.github/workflows/awstest.yml +++ b/nf_core/pipeline-template/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action {%- raw %} - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2.0.0 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} From d24652af1f7e9dd657bfe0d68b4b637b0c2125b9 Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Thu, 8 Jun 2023 16:52:52 +0100 Subject: [PATCH 4/5] Use specific Nextflow + nf-amazon version to get check if tests pass --- .github/workflows/create-test-wf.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 8f3c5fdb47..d52fa22301 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -23,8 +23,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" - - "latest-everything" + - "23.04.1" steps: - uses: actions/checkout@v3 name: Check out source-code repository @@ -47,7 +46,7 @@ jobs: - name: Run nf-core/tools run: | nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain - nextflow run nf-core-testpipeline -profile test,docker --outdir ./results + nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2 - name: Upload log file artifact if: ${{ always() }} From 51882b2559ed06fe7c9321ff7c0601e1ee8240cc Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Fri, 9 Jun 2023 09:19:05 +0100 Subject: [PATCH 5/5] Revert "Use specific Nextflow + nf-amazon version to get check if tests pass" This reverts commit d24652af1f7e9dd657bfe0d68b4b637b0c2125b9. --- .github/workflows/create-test-wf.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index d52fa22301..8f3c5fdb47 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -23,7 +23,8 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.1" + - "22.10.1" + - "latest-everything" steps: - uses: actions/checkout@v3 name: Check out source-code repository @@ -46,7 +47,7 @@ jobs: - name: Run nf-core/tools run: | nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain - nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2 + nextflow run nf-core-testpipeline -profile test,docker --outdir ./results - name: Upload log file artifact if: ${{ always() }}