-
Notifications
You must be signed in to change notification settings - Fork 75
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #159 from nf-core/dev
Dev -> Master for 1.10.0 release
- Loading branch information
Showing
48 changed files
with
588 additions
and
343 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
|
|
||
| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@v7 | ||
| with: | ||
| stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." | ||
| stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: "${{ secrets.GITHUB_TOKEN }}" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| name: full-sized tests on cloud providers | ||
| run-name: Submitting workflow to all cloud providers using full sized data | ||
| on: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
| inputs: | ||
| platform: | ||
| description: "Platform to run test" | ||
| required: true | ||
| default: "all" | ||
| type: choice | ||
| options: | ||
| - all | ||
| - aws | ||
| - azure | ||
| - gcp | ||
| jobs: | ||
| run-full-tests-on-aws: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "aws_fetchngs_full" | ||
| profiles: test_full,public_aws_ecr | ||
| parameters: | | ||
| { | ||
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | ||
| "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log | ||
| run-full-tests-on-gcp: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_GCP_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "gcp_fetchngs_full" | ||
| profiles: test_full | ||
| parameters: | | ||
| { | ||
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | ||
| "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log | ||
| run-full-tests-on-azure: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "azure_fetchngs_full" | ||
| profiles: test_full | ||
| parameters: | | ||
| { | ||
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | ||
| "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| name: small-sized tests on cloud providers | ||
| run-name: Submitting workflow to all cloud providers using small sized data | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| platform: | ||
| description: "Platform to run test" | ||
| required: true | ||
| default: "all" | ||
| type: choice | ||
| options: | ||
| - all | ||
| - aws | ||
| - azure | ||
| - gcp | ||
| jobs: | ||
| run-small-tests-on-aws: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "aws_fetchngs_small" | ||
| profiles: test,public_aws_ecr | ||
| parameters: | | ||
| { | ||
| "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log | ||
| run-small-tests-on-gcp: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_GCP_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "gcp_fetchngs_small" | ||
| profiles: test | ||
| parameters: | | ||
| { | ||
| "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-test-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log | ||
| run-small-tests-on-azure: | ||
| if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }} | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: seqeralabs/action-tower-launch@v1 | ||
| with: | ||
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | ||
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | ||
| compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }} | ||
| workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/fetchngs/work-${{ github.sha }}" | ||
| run_name: "azure_fetchngs_small" | ||
| profiles: test | ||
| parameters: | | ||
| { | ||
| "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-test-${{ github.sha }}" | ||
| } | ||
| - uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Tower debug log file | ||
| path: tower_action_*.log |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v2.7.1" | ||
| hooks: | ||
| - id: prettier |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.