Skip to content

Commit ca7d3b6

Browse files
maxulyssemaxulysse
committed
Merge branch 'dev' into nf-core-template-merge-3.3.1
2 parents 949f8fc + 21acf5a commit ca7d3b6

File tree

601 files changed

+104597
-440
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

601 files changed

+104597
-440
lines changed

‎.github/include.yaml‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
".":
2+
- ./.github/workflows/**
3+
- ./nf-test.config
4+
- ./nextflow.config
5+
tests:
6+
- ./assets/*
7+
- ./bin/*
8+
- ./conf/*
9+
- ./main.nf
10+
- ./nextflow_schema.json

‎.github/workflows/awsfulltest.yml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,9 @@ jobs:
1616
# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
1717
if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
1818
runs-on: ubuntu-latest
19+
strategy:
20+
matrix:
21+
aligner: ["star_salmon", "star_rsem"]
1922
steps:
2023
- name: Set revision variable
2124
id: revision
@@ -36,6 +39,7 @@ jobs:
3639
parameters: |
3740
{
3841
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
42+
"aligner": "${{ matrix.aligner }}",
3943
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}"
4044
}
4145
profiles: test_full

‎.github/workflows/cloud_tests_full.yml‎

Lines changed: 97 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,97 @@
1+
name: full-sized tests on cloud providers
2+
run-name: Submitting workflow to all cloud providers using full sized data
3+
on:
4+
workflow_dispatch:
5+
inputs:
6+
platform:
7+
description: "Platform to run test"
8+
required: true
9+
default: "all"
10+
type: choice
11+
options:
12+
- all
13+
- aws
14+
- azure
15+
- gcp
16+
jobs:
17+
run-full-tests-on-aws:
18+
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
19+
runs-on: ubuntu-latest
20+
strategy:
21+
matrix:
22+
aligner: ["star_salmon", "star_rsem"]
23+
steps:
24+
- uses: seqeralabs/action-tower-launch@v2
25+
with:
26+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
27+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
28+
compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
29+
workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
30+
run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
31+
revision: ${{ github.sha }}
32+
profiles: test_full_aws
33+
parameters: |
34+
{
35+
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
36+
"aligner": "${{ matrix.aligner }}",
37+
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
38+
}
39+
- uses: actions/upload-artifact@v3
40+
with:
41+
name: Tower debug log file
42+
path: tower_action_*.log
43+
44+
run-full-tests-on-azure:
45+
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
46+
runs-on: ubuntu-latest
47+
strategy:
48+
matrix:
49+
aligner: ["star_salmon", "star_rsem"]
50+
steps:
51+
- uses: seqeralabs/action-tower-launch@v2
52+
with:
53+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
54+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
55+
compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
56+
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
57+
run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
58+
revision: ${{ github.sha }}
59+
profiles: test_full_azure
60+
parameters: |
61+
{
62+
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
63+
"aligner": "${{ matrix.aligner }}",
64+
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
65+
"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
66+
}
67+
- uses: actions/upload-artifact@v3
68+
with:
69+
name: Tower debug log file
70+
path: tower_action_*.log
71+
72+
run-full-tests-on-gcp:
73+
if: ${{ github.event.inputs.platform == 'gcp' || !github.event.inputs }}
74+
runs-on: ubuntu-latest
75+
strategy:
76+
matrix:
77+
aligner: ["star_salmon", "star_rsem"]
78+
steps:
79+
- uses: seqeralabs/action-tower-launch@v2
80+
with:
81+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
82+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
83+
compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
84+
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
85+
run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
86+
revision: ${{ github.sha }}
87+
profiles: test_full_gcp
88+
parameters: |
89+
{
90+
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
91+
"aligner": "${{ matrix.aligner }}",
92+
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
93+
}
94+
- uses: actions/upload-artifact@v3
95+
with:
96+
name: Tower debug log file
97+
path: tower_action_*.log

‎.github/workflows/cloud_tests_small.yml‎

Lines changed: 81 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,81 @@
1+
name: small-sized tests on cloud providers
2+
run-name: Submitting workflow to all cloud providers using small sized data
3+
on:
4+
workflow_dispatch:
5+
inputs:
6+
platform:
7+
description: "Platform to run test"
8+
required: true
9+
default: "all"
10+
type: choice
11+
options:
12+
- all
13+
- aws
14+
- azure
15+
- gcp
16+
jobs:
17+
run-small-tests-on-aws:
18+
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
19+
runs-on: ubuntu-latest
20+
steps:
21+
- uses: seqeralabs/action-tower-launch@v2
22+
with:
23+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
24+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
25+
compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
26+
workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
27+
run_name: "aws_rnaseq_small"
28+
revision: ${{ github.sha }}
29+
profiles: test
30+
parameters: |
31+
{
32+
"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}/"
33+
}
34+
- uses: actions/upload-artifact@v3
35+
with:
36+
name: Tower debug log file
37+
path: tower_action_*.log
38+
39+
run-small-tests-on-azure:
40+
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
41+
runs-on: ubuntu-latest
42+
steps:
43+
- uses: seqeralabs/action-tower-launch@v2
44+
with:
45+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
46+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
47+
compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
48+
workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
49+
run_name: "azure_rnaseq_small"
50+
revision: ${{ github.sha }}
51+
profiles: test
52+
parameters: |
53+
{
54+
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
55+
}
56+
- uses: actions/upload-artifact@v3
57+
with:
58+
name: Tower debug log file
59+
path: tower_action_*.log
60+
61+
run-small-tests-on-gcp:
62+
if: ${{ github.event.inputs.platform == 'gcp' }}
63+
runs-on: ubuntu-latest
64+
steps:
65+
- uses: seqeralabs/action-tower-launch@v2
66+
with:
67+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
68+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
69+
compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
70+
workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
71+
run_name: "gcp_rnaseq_small"
72+
revision: ${{ github.sha }}
73+
profiles: test
74+
parameters: |
75+
{
76+
"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
77+
}
78+
- uses: actions/upload-artifact@v3
79+
with:
80+
name: Tower debug log file
81+
path: tower_action_*.log

‎.gitignore‎

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,13 @@
1+
*.pyc
2+
.DS_Store
13
.nextflow*
2-
work/
4+
.nf-test.log
35
data/
6+
nf-test
7+
.nf-test*
48
results/
5-
.DS_Store
6-
testing/
9+
test.xml
710
testing*
8-
*.pyc
11+
testing/
12+
work/
913
null/

0 commit comments

Comments
 (0)