-
Notifications
You must be signed in to change notification settings - Fork 78
146 lines (144 loc) · 6.73 KB
/
cloud_tests_full.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
name: nf-core cloud full size tests
# This workflow is triggered on PRs opened against the master branch.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on Cloud
run-name: Submitting workflow to all cloud providers using full sized data
on:
pull_request:
branches:
- master
pull_request_review:
types: [submitted]
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:
name: Run AWS full tests
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }} || github.repository == 'nf-core/fetchngs' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
strategy:
matrix:
download_method: ["aspera", "ftp", "sratools"]
steps:
- uses: octokit/[email protected]
id: check_approvals
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- id: test_variables
if: github.event_name != 'workflow_dispatch'
run: |
JSON_RESPONSE='${{ 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
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
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-${{ github.sha }}"
run_name: "aws_fetchngs_full_${{ matrix.download_method }}"
revision: ${{ github.sha }}
profiles: test_full
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"download_method": "${{ matrix.download_method }}",
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-full-tests-on-azure:
name: Run Azure full tests
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }} || github.repository == 'nf-core/fetchngs' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
strategy:
matrix:
download_method: ["aspera", "ftp", "sratools"]
steps:
- uses: octokit/[email protected]
id: check_approvals
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- id: test_variables
if: github.event_name != 'workflow_dispatch'
run: |
JSON_RESPONSE='${{ 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
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
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-${{ github.sha }}"
run_name: "azure_fetchngs_full_${{ matrix.download_method }}"
revision: ${{ github.sha }}
profiles: test_full
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"download_method": "${{ matrix.download_method }}",
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
run-full-tests-on-gcp:
name: Run GCP full tests
if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }} || github.repository == 'nf-core/fetchngs' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
strategy:
matrix:
download_method: ["aspera", "ftp", "sratools"]
steps:
- uses: octokit/[email protected]
id: check_approvals
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- id: test_variables
if: github.event_name != 'workflow_dispatch'
run: |
JSON_RESPONSE='${{ 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
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
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-${{ github.sha }}"
run_name: "gcp_fetchngs_full_${{ matrix.download_method }}"
revision: ${{ github.sha }}
profiles: test_full
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"download_method": "${{ matrix.download_method }}",
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/fetchngs/results-${{ github.sha }}/download_method_${{ matrix.download_method }}/"
}
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log